Genomewide Unbiased Identification of DSBs Evaluated by Sequencing (GUIDE-Seq)

ABSTRACT

Unbiased, genomewide and highly sensitive methods for detecting mutations, e.g., off-target mutations, induced by engineered nucleases.

CLAIM OF PRIORITY

This application is a continuation of U.S. patent application Ser. No. 15/192,753, filed Jun. 24, 2016; which is a continuation of PCT/US2015/037269, filed on Jun. 23, 2015, which claims the benefit of U.S. Provisional Patent Applications Ser. No. 62/015,911, filed on Jun. 23, 2014; 62/077,844, filed on Nov. 10, 2014; 62/078,923, filed on Nov. 12, 2014; and 62/088,223, filed on Dec. 5, 2014. The entire contents of the foregoing are hereby incorporated by reference.

FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

This invention was made with Government support under Grant No. GM105378 awarded by the National Institutes of Health. The Government has certain rights in the invention.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has been submitted electronically in ASCII format and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Oct. 11, 2017, is named 40978-0015002_SL.txt and is 194,795 bytes in size.

TECHNICAL FIELD

Provided are highly sensitive, unbiased, and genome-wide methods for identifying the locations of engineered nuclease cleavage sites in living cells.

BACKGROUND

A long-held goal of human medicine has been to treat inherited genetic disorders. Genome editing encompasses the powerful concept of directly correcting mutations in endogenous genes to cure or prevent disease. An emerging example of this approach is the clinical trial of a zinc finger nuclease (ZFN) therapeutic engineered to disrupt CCR5, a co-receptor for HIV (1). This ex vivo autologous cell therapy approach attempts to recapitulate the successful cure of HIV in Timothy Brown, the “Berlin Patient,” who was transplanted with bone marrow cells from an individual bearing homozygous mutations in CCR5. Another recent example is the correction of X-linked severe combined immunodeficiency disorder by gene targeting with ZFNs in hematopoietic stem cells derived from a 6-month old subject (2).

There are four main classes of engineered nucleases: 1) meganucleases, 2) zinc-finger nucleases, 3) transcription activator effector-like nucleases (TALEN), and 4) Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) Cas RNA-guided nucleases (RGN).

However, adoption of these new therapeutic and research tools may depend on a demonstration of their specificity. Understanding and identifying off-target effects in human and other eukaryotic cells will be critically essential if these nucleases are to be used widely for research and therapeutic applications.

SUMMARY

GUIDE-Seq provides an unbiased, genomewide and highly sensitive method for detecting mutations, e.g., off-target mutations, induced by engineered nucleases. Thus, the method provides the most comprehensive unbiased method for assessing mutations on a genomewide scale in living mammalian cells. The method can be utilized in any cell type in which dsODNs can be efficiently captured into nuclease-induced DSBs.

Thus, in one aspect, the invention provides methods for detecting double stranded breaks (DSBs), e.g., off-target DSBs, e.g., induced by an exogenous engineered nucleases in genomic DNA of a cell. The methods include contacting the cell with a double-stranded oligodeoxynucleotide (dsODN), preferably wherein the dsODN is between 15 and 75 nts long, e.g., 15-50 nts, 50-75 nts, 30-35 nts, 60-65 nts, or 50-65 nts long, wherein both strands of the dsODN are orthogonal to the genome of the cell; preferably, the 5′ ends of the dsODN are phosphorylated; and also preferably, phosphorothioate linkages are present on both 3′ ends, or two phosphorothioate linkages are present on both 3′ ends and both 5′ ends;

expressing or activating the exogenous engineered nuclease in the cell, for a time sufficient for the nuclease to induce DSBs in the genomic DNA of the cell, and for the cell to repair the DSBs, integrating a dsODN at one or more DSBs; amplifying a portion of genomic DNA comprising an integrated dsODN; and sequencing the amplified portion of the genomic DNA, thereby detecting a DSB in the genomic DNA of the cell.

In some embodiments, amplifying a portion of the genomic DNA comprises:

fragmenting the DNA, e.g., by shearing; ligating ends of the fragmented genomic DNA from the cell with a universal adapter; performing a first round of polymerase chain reaction (PCR) on the ligated DNA with a primer complementary to the integrated dsODN (primer A) and a primer complementary to the universal adapter (primer B); then performing a second round of PCR using a 3′ nested primer complementary to primer A (primer C), a 3′ nested primer complementary to primer B (primer D), and a primer complementary to primer D (primer E). In some embodiments, primer E comprises one or more of: a purification or binding sequence, e.g., a flow-cell binding sequence; and an identification sequence, e.g., a barcode or random molecular index.

In some embodiments, the engineered nuclease is selected from the group consisting of meganucleases, zinc-finger nucleases, transcription activator effector-like nucleases (TALEN), and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas RNA-guided nucleases (CRISPR/Cas RGNs).

In another aspect, the invention provides methods for determining which of a plurality of guide RNAs is most specific, i.e., induces the fewest off-target DSBs. The methods include contacting a first population of cells with a first guide RNA and a double-stranded oligodeoxynucleotide (dsODN), preferably wherein the dsODN is between 15 and 75 nts long, e.g., 15-50 nts, 50-75 nts, 60-65 nts, 30-35 nts or 50-65 nts long, wherein both strands of the dsODN are orthogonal to the genome of the cell; preferably, the 5′ ends of the dsODN are phosphorylated; and also preferably, phosphorothioate linkages are present on both 3′ ends, or two phosphorothioate linkages are present on both 3′ ends and both 5′ ends;

expressing or activating an exogenous Cas9 engineered nuclease in the first population of cells, for a time sufficient for the nuclease to induce DSBs in the genomic DNA of the cells, and for the cells to repair the DSBs, integrating a dsODN at one or more DSBs; amplifying a portion of genomic DNA from the first population of cells comprising an integrated dsODN; and sequencing the amplified portion of the genomic DNA from the first population of cells; determining a number of sites at which the dsODN integrated into the genomic DNA of the first population of cells; contacting a second population of cells with a second guide RNA and a double-stranded oligodeoxynucleotide (dsODN), preferably wherein the dsODN is between 15 and 75 nts long, e.g., 15-50 nts, 50-75 nts, 30-35 nts, 60-65 nts, or 50-65 nts long, wherein both strands of the dsODN are orthogonal to the genome of the cell; preferably, the 5′ ends of the dsODN are phosphorylated; and also preferably, two phosphorothioate linkages are present on both 3′ ends and both 5′ ends; expressing or activating an exogenous Cas9 engineered nuclease in the second population of cells, for a time sufficient for the nuclease to induce DSBs in the genomic DNA of the second population of cells, and for the cells to repair the DSBs, integrating a dsODN at one or more DSBs; amplifying a portion of genomic DNA comprising an integrated dsODN from the second population of cells; and sequencing the amplified portion of the genomic DNA from the second population of cells; determining a number of sites at which the dsODN integrated into the genomic DNA of the second population of cells; comparing the number of sites at which the dsODN integrated into the genomic DNA of the first population of cells to the number of sites at which the dsODN integrated into the genomic DNA of the second population of cells; wherein the dsODN that integrated at fewer (off-target) sites is more specific. The methods can be repeated for a third, fourth, fifth, sixth, or more populations of cells. “Fewer” off target sites can include both a lesser number of DSB sites and/or reduced frequency of occurrence of a DSB at (one or more) individual sites.

Also provided herein are methods for efficiently integrating a short dsDNA of interest into the site of a DSB by use of an end-protected dsODN as described herien.

In some embodiments, the cell is a mammalian cell.

In some embodiments, wherein the engineered nuclease is a Cas9 nuclease, and the methods also include expressing in the cells a guide RNA, e.g., a single guide or a tracrRNA/crRNA pair, that directs the Cas9 nuclease to a target sequence in the genome.

In some embodiments, the dsODN is biotinylated, e.g., comprises biotin covalently attached to the dsODN, and/or comprises a randomized DNA barcode or Cre or Lox site. The method of any of the above claims, wherein the dsODN is biotinylated.

In some embodiments, the methods described herein include shearing the genomic gDNA into fragments; and isolating fragments comprising a dsODN by binding to the biotin.

In some embodiments, the dsODN is blunt-ended or has 1, 2, 3, or 4 nts overhanging on the 5′ end; is phosphorylated on the 5′ ends; and/or is phosphorothioated on the 3′ ends.

In some embodiments, the dsODN is blunt-ended, is phosphorylated on the 5′ ends, and is phosphorothioated on the 3′ ends.

In some embodiments, the dsODN contains a randomized DNA barcode, Lox recognition site, restriction enzyme recognition site, and/or tag sequence.

In some embodiments, the methods include shearing the genomic gDNA into fragments; and preparing the fragments for sequencing, e.g., high-throughput sequencing, by end-repair/a-tailing/ligation of a sequencing adapter, e.g., a single-tailed sequencing adapter.

In some embodiments, the DSB is a background genomic DSB (e.g., at a fragile site) or a DSB caused by small-molecule inhibitors of key cellular proteins.

Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Methods and materials are described herein for use in the present invention; other, suitable methods and materials known in the art can also be used. The materials, methods, and examples are illustrative only and not intended to be limiting. All publications, patent applications, patents, sequences, database entries, and other references mentioned herein are incorporated by reference in their entirety. In case of conflict, the present specification, including definitions, will control.

Other features and advantages of the invention will be apparent from the following detailed description and figures, and from the claims.

DESCRIPTION OF DRAWINGS

FIGS. 1A-B. Optimization of CRISPR-Cas nuclease-mediated dsODN capture. (A) The sequence of the short oligonucleotide tag used is shown (SEQ ID NOs:1-2, respectively, in order of appearance). All oligonucleotides used are 5′ phosphorylated. The tag oligonucleotide also contains a diagnostic NdeI restriction sites that enables estimation of integration frequencies by RFLP. (B) The bottom graph shows integration (%) of the short dsODN by RFLP. The integration rate for dsODNs with both 5′ and 3′ phosphorothioate linkages (left hand bar in each set) is compared with dsODNs with only 5′ phosphorothioate linkage (middle bar in each set) and control without dsODN (right hand bar in each set).

FIGS. 2A-B. Characterization of integration for VEGF site 1. (A) RFLP assay is shown for VEGF site 1, as analyzed on a QIAXCEL capillary electrophoresis instrument, demonstrating successful incorporation of the dsODN bearing the NdeI restriction site. (B) Sanger sequencing data is shown for dsODN integrations at the intended VEGF site 1 target site (SEQ ID NOs:90-103, in order of appearance). The dsODN sequence is highlighted in grey. The site recognized by the guide RNA/Cas9 complex targeted to VEGFA site 1 is highlighted in bold text with the adjacent protospacer adjacent motif (PAM) sequence underlined. The location of the expected double-stranded break induced by Cas9 at this site is indicated with a small black arrow.

FIG. 3. Overview of exemplary GUIDE-seq method.

FIGS. 4A-E. CRISPR-Cas off-target cleavage sites discovered by GUIDE-Seq method. Data is shown for four sites, VEGF sites 1-3 (VEGF Site 1: SEQ ID NOS 37 and 104-118, respectively, in order of appearance; VEGF Site 2: SEQ ID NOS 38 and 119-220, respectively, in order of appearance; VEGF Site 3: SEQ ID NOS 39 and 221-260, respectively, in order of appearance), and EMX1 (EMX1: SEQ ID NOS 36 and 261-272, respectively, in order of appearance). Mismatches to the target site sequence are highlighted. A small solid black arrow is used to indicate the intended on-target site, while a small dashed arrow is used to mark known off-target sites that had been detected in an earlier study (Fu et al., 2013).

FIGS. 5A-I. Design, optimization and application of an exemplary GUIDE-Seq method.

(A) Schematic overview of an exemplary GUIDE-Seq method.

(B) Optimization of dsODN integration into RGN-induced DSBs in human cells. Rates of integration for different modified oligonucleotides as measured by RFLP assay are shown. Control reactions were transfected with only the RGN-encoding plasmids (i.e., without dsODN).

(C) Schematic illustrating how mapping of genomic sequence reads enabled identification of DSB position. Bidirectionally mapping reads or reads mapping to the same direction but amplified by different primers are signatures of DSBs in the GUIDE-seq assay. See also FIG. 1A.

(D) GUIDE-Seq-based identification of RGN-induced DSBs. Start sites of GUIDE-Seq reads mapped to genome enable mapping of the DSB to within a few base pairs. Mapped reads for the on-target sites of the ten RGNs we assessed by GUIDE-Seq are shown. In all cases, the target site sequence is shown with the 20 bp protospacer sequence to the left and the PAM sequence to the right on the x-axis. Note how in all cases the highest peak falls within 3 to 4 bps of the 5′-edge of the NGG PAM sequence, the expected position of an RGN cleavage event.

TARGET SITE SEQ ID NO: VEGFA SITE 1 273 VEGFA SITE 2 274 RNF2 275 HEK293 SITE 1 276 VEGFA SITE 3 277 EMX1 278 HEK293 SITE 2 279 HEK293 SITE 3 280 FANCF 281 HEK293 SITE 4 282

(E) Numbers of previously known and novel off-target cleavage sites identified by GUIDE-Seq for the ten RGNs analyzed in this study. All previously known off-target cleavage for 4 RGNs were identified by GUIDE-seq.

(F) Scatterplot of on-target site orthogonality to the human genome (y-axis) versus total number of off-target sites detected by GUIDE-Seq for the ten RGNs of this report. Orthogonality was calculated as the total number of sites in the human genome bearing 1 to 6 mismatches relative to the on-target site.

(G) Scatterplot of on-target site GC content (y-axis) versus total number of off-target sites detected by GUIDE-Seq for the ten RGNs of this report.

(H) Chromosome ideogram of CRISPR/Cas9 on- and off-target sites for the RGN that targets EMX1. Additional ideograms for the remaining RGNs can be found in FIG. 13.

(I) Genomic locations of off-target cleavage sites identified by GUIDE-Seq for the ten RGNs examined in this study.

FIGS. 6A-J. Sequences of off-target sites identified by GUIDE-Seq for ten RGNs. For each RGN, the intended target sequence is shown in the top line with cleaved sites shown underneath and with mismatches to the on-target site shown and highlighted in color. GUIDE-Seq sequencing read counts are shown to the right of each site. The on-target site is marked with a square and previously known off-target sites with a diamond. Data is shown for RGNs targeting the following sites: (A) VEGFA site 1 (SEQ ID NOs:37 and 283-304, respectively, in order of appearance), (B) VEGFA site 3 (SEQ ID NOs:39 and 305-364, respectively, in order of appearance), (C) VEGFA site 2 (SEQ ID NOs:38 and 365-516, respectively, in order of appearance), (D) EMX1 (SEQ ID NOs:36 and 517-532, respectively, in order of appearance), (E) FANCF (SEQ ID NOs:41 and 533-541, respectively, in order of appearance), (F) HEK293 site 1 (SEQ ID NOs:42 and 542-551, respectively, in order of appearance), (G) HEK293 site 2 (SEQ ID NOs:43 and 552-554, respectively, in order of appearance), (H) HEK293 site 3 (SEQ ID NOs:44 and 555-560, respectively, in order of appearance), (I) HEK293 site 4 (SEQ ID NO:45 and 561-694, respectively, in order of appearance), (J) RNF2 (SEQ ID NOs:40 and 695, respectively, in order of appearance). No off-target sites were found for the RGN targeted to the RNF2 site.

FIGS. 7A-F. GUIDE-Seq cleavage sites are bona fide RGN off-target mutation sites.

(A) Schematic overview of the AMP-based sequencing method used to confirm indel mutations at GUIDE-Seq cleavage sites is shown in the top half of the figure. Histogram plots of mapped indel mutations are shown for three RGN on-target sites. Deletions are shown above the X-axis whereas insertions are shown below. Boundaries of the overall target site (i.e., protospacer and PAM sequence) are shown with dotted lines and the boundary between the protospacer and PAM sequence is shown as a dotted line between the other two. RGN cleavage is predicted to occur 3 to 4 bps from the 5′ edge of the protospacer.

(B)-(F) Scatterplots of indel frequencies (x-axis) and GUIDE-Seq sequencing read counts (y-axis) for cleavage sites identified by GUIDE-Seq for RGNs targeted to: VEGFA site 1, VEGFA site 2, VEGFA site 3, EMX1, and FANCF.

FIG. 8A-E Analysis of RGN-induced off-target sequence characteristics

(A) Fraction of potential RGN off-target sites bearing a certain number of mismatches that are cleaved (as detected by GUIDE-Seq).

(B) Plots of GUIDE-Seq read counts (log-scale) for RGN off-target cleavage sites bearing a certain number of mismatches

(C) Effects of mismatch position within the protospacer on GUIDE-Seq read counts for RGN off-target sites. Bases are numbered 1 to 20 with 20 being the base adjacent to the PAM.

(D) Effects of wobble transition, non-wobble transition, and transversion mismatches estimated by linear regression analysis.

(E) Fraction of GUIDE-Seq read count variance explained by individual univariate analyses for the effect of mismatch number, mismatch type, mismatch position, PAM density, expression level, and genomic position (intergenic/exon/intron).

FIGS. 9A-F. Comparisons of GUIDE-Seq with computational prediction or ChIP-Seq methods for identifying RGN off-target sites

(A) Venn diagrams illustrating overlap between off-target sites predicted by the MIT CRISPR Design Tool and GUIDE-Seq for nine RGNs.

(B) Venn diagrams illustrating overlap between off-target sites predicted by the E-CRISP computational prediction program and GUIDE-Seq for nine RGNs.

(C) Histogram showing the numbers of bona fide RGN off-target sites identified by GUIDE-Seq that are predicted, not predicted, and not considered by the MIT CRISPR Design Tool. Sites predicted by the MIT CRISPR Design Tool are divided into quintiles based on the score provided by the program. Each bar has the sites sub-classified based on the number of mismatches relative to the on-target site. Bulge sites are those that have a skipped base position at the gRNA-protospacer DNA interface.

(D) Histogram showing the numbers of bona fide RGN off-target sites identified by GUIDE-Seq that are predicted, not predicted, and not considered by the E-CRISP computational prediction tool. Sites are subdivided as described in (c).

(E) Venn diagrams illustrating overlap between dCas9 binding sites identified by ChIP-Seq and RGN off-target cleavage sites identified by GUIDE-Seq.

(F) Histogram plots of RGN off-target sites identified by GUIDE-Seq and dCas9 binding sites identified by ChIP-Seq classified by the number of mismatches in the sequence relative to the intended on-target site. Kernel density estimation of GUIDE-Seq and ChIP-Seq mismatches is depicted. Dotted lines indicate the mean number of mismatches for each class of sites.

FIG. 10A-F Large-scale structural alterations induced by RGNs

(A) Schematic overview of AMP strategy for detecting translocations. Additional details in Methods.

(B) Circos plots of structural variation induced by RGNs. Data for five RGNs and a control of cells are shown. Chromosomes are arranged in a circle with translocations shown as arcs between two chromosomal locations. Deletions or inversions greater than 1 kb in length are shFwn as straight lines. Sites that are not on-target, off-target, or breakpoint hotspots are classified as “other”.

(C) Example of a translocation detected between the VEGFA site 1 on-target site on chromosome 6 and an off-target site on chromosome 17. All four possible reciprocal translocations were detected using AMP.

(D) Examples of large deletion and inversion between two off-target sites in VEGFA site 2 detected by AMP. Sequences in section 1 disclosed as SEQ ID NOS 696-703, respectively, in order of appearance, sequences in section 2 disclosed as SEQ ID NOS 704-711, respectively, in order of appearance, sequences in section 3 disclosed as SEQ ID NOS 712-717, respectively, in order of appearance, and sequences in section 4 disclosed as SEQ ID NOS 718-726, respectively, in order of appearance.

(E) Summary table of different RGN-induced and RGN-independent structural variations observed with five RGNs. Controls with Cas9 only, dsODN oligo only, and cells only are also shown. Sequences in section labeled “large deletion” disclosed as SEQ ID NOS 727-728, respectively, in order of appearance and sequences in section labeled “inversion” disclosed as SEQ ID NOS 729-736, respectively, in order of appearance.

(F) Chromosome ideogram illustrating the locations of breakpoint hotspots in U2OS and HEK293 cells. Two hotspots overlap at the centromeric regions of chromosomes 1 and 10.

FIG. 11A-H. GUIDE-Seq profiles of RGNs directed by tru-gRNAs

(A) Numbers of previously known and novel off-target cleavage sites identified for RGNs directed to the to VEGFA site 1, VEGFA site 3, and EMX1 target sites by matched full-length gRNAs and truncated gRNAs. Note that the data for the RGNs directed by full-length gRNAs are the same as those presented in FIGS. 1e and is shown again here for ease of comparison.

(B)-(D) Chromosome ideograms showing on- and off-target sites for RGNs directed to the VEGFA site 1, VEGFA site 3, and EMX1 target sites by matched full-length gRNAs and truncated gRNAs. Note that the ideograms for the RGNs directed by full-length gRNAs are the same as those presented in FIG. 1h and FIGS. 13A-B and are shown again here for ease of comparison.

(E) GUIDE-Seq-based identification of DSBs induced by RGNs directed by tru-gRNAs. Mapped reads for the on-target sites of the three RGNs directed by tru-gRNAs we assessed by GUIDESeq are shown (SEQ ID NOS 737-739, respectively, in order of appearance). In all cases, the target site sequence is shown with the 20 bp protospacer sequence to the left and the PAM sequence to the right on the x-axis. As with RGNs directed by full-length gRNAs, note how the highest peak falls within 3 to 4 bps of the 5′-edge of the NGG PAM sequence, the expected position of an RGN cleavage event.

(F)-(H) Sequences of off-target sites identified by GUIDE-Seq for RGNs directed by tru-gRNAs. For each RGN, the intended target sequence is shown in the top line with cleaved sites shown underneath and with mismatches to the on-target site shown and highlighted in color. GUIDESeq sequencing read counts are shown to the right of each site. The intended on-target site is marked with a square, previously known off-target sites of RGNs directed by both a full length gRNA and a tru-gRNA are marked with a dark grey diamond, and previously known off-target sites found only with RGNs directed by a tru-gRNA are marked with a light grey diamond. Previously known off-target sites were those that were shown to have a mutagenesis frequency of 0.1% or higher in an earlier report FU et al., Nat Biotechnol 32, 279-284 (2014)). Data is shown for RGNs directed by tru-gRNAs to the (f) VEGFA site 1 (SEQ ID NOS 87 and 740-749, respectively, in order of appearance), (g) VEGFA site 3 (SEQ ID NOS 88 and 750-765, respectively, in order of appearance), and (h) EMX1 (SEQ ID NOS 89 and 766-769, respectively, in order of appearance) target sites.

FIG. 12. Detailed schematic overview of GUIDE-Seq and AMP-based sequencing for validation of dsODN insertions and indel mutations. Details for both protocols can be found in Methods.

FIG. 13A-J. Chromosome ideograms of CRISPR/Cas9 on- and off-target sites for all ten RGNs evaluated by GUIDE-Seq

FIG. 14. Multi-factor linear regression model to show independent effects of factors on GUIDE-Seq read count

FIGS. 15A-D. Histogram plots of mapped indel mutations for seven ChIP-Seq binding sites previously characterized as off-target cleavage sites Experimental and control samples are shown side-by-side for each site.

FIG. 16A is a graph showing integration frequencies of 3 types of dsODNs using TALENs, ZFNs, and RFNs targeted against EGFP. All of the dsODNs were 5′ phosphorylated. The dsODNs had either a randomized 5′- or 3′-4-bp overhang or were blunt, as indicated.

FIGS. 16B-C are graphs showing efficient integration of a blunt, 5′-phosphorylated, 34-bp double-stranded oligodeoxynucleotide (dsODN) (oSQT685/686) into double-stranded breaks (DSBs) induced by TALENs at 2 endogenous target sites, CCR5 and APC in U2OS cells. (16B) RFLP analysis shows % integration of dsODN tag oSQT685/686 into DSBs induced by TALENs at 2 endogenous sites, CCR5 and APC. (16C) Cumulative mutagenesis frequencies are measured by T7E1 assay at these 2 endogenous target sites.

FIGS. 17A and 17B are bar graphs showing a comparison of different dsODN end protections; dsODNs used in this experiment were phosphorylated and blunt and had either both 5′ and 3′ phosphorothioate modifications, or only 3′ phosphorothioate modifications. 17A, RFNs in human U2OS cells; 17B, Cas9 in mouse ES cells.

FIGS. 18A-B are graphs showing experiments at different concentrations of 3′ phosphorothioate modified oligo in mouse ES cells. 18A, Nanog sgRNA/Cas9; 18B, Phc1 sgRNA/Cas9. The dsODNs were phosphorylated and blunt and had either both 5′ and 3′ phosphorothioate modifications, or only 3′ phosphorothioate modifications. The experiments were conducted with dimeric RNA-guided FokI nucleases in human U2OS cells (FIG. 18A), or with standard Cas9 in mouse ES cells (FIG. 18B).

FIG. 18C is a graph showing T7E1 analysis of the rate of disruption in the presence of 3′ phosphorothioate modified oligo in mouse ES cells.

FIGS. 19A-B show efficient integration of biotinylated dsODN tags into double-stranded breaks (DSBs) induced by Cas9 at 3 endogenous target sites, VEGFA3, EMX1, and FANCF1 in U2OS cells. (19A) RFLP analysis shows % integration rates of biotinylated dsODN (oSQT1261/1262), compared to the standard dsODN (oSQT685/686) into DSBs induced by Cas9 at 3 endogenous sites, VEGFA3, EMX1, and FANCF1 in U2OS cells. (19B) T7EI shows % estimated mutagenesis frequencies with biotinylated dsODN (oSQT1261/1262), compared to the standard dsODN (oSQT685/686) at 3 endogenous sites, VEGFA3, EMX1, and FANCF1 in U2OS cells.

FIGS. 20A-B show that longer dsODN tags can be optimized to integrate efficiently at sites of CRISPR-Cas9 induced DSBs. (20A) RFLP analysis shows % integration rates of 60-bp dsODNs (oSQT1255/1256, oSQT1257/1258, and oSQT1259/1260) when being transfected with 75, 50, or 25 pmol. Tested at 2 endogenous sites, EMX1 and FANCF1 in U2OS cells. (20B) T7EI shows % estimated NHEJ rates of 60-bp dsODNs (oSQT1255/1256, oSQT1257/1258, oSQT1259/1260 when being transfected with 75, 50, or 25 pmol. Tested at 2 endogenous sites, EMX1 and FANCF1 in U2OS cells.

FIG. 21 is a graph showing the number of off-target cleavage sites identified by GUIDE-seq for the engineered VQR and VRER SpCas9 variants using different sgRNAs.

FIG. 22 is a graph summarizing GUIDE-seq detected changes in specificity between wild-type and D1135E SpCas9 variants at off-target sites. Estimated fold-gain in specificity at sites without read-counts for D1135E are not plotted.

FIGS. 23A-B are graphs showing (23A) Mean frequency of GUIDE-seq oligo tag integration at the on-target sites, estimated by restriction fragment length polymorphism analysis. Error bars represent s.e.m., n=4; (23B) Mean mutagenesis frequencies at the on-target sites detected by T7E1 for GUIDE-seq experiments. Error bars represent s.e.m., n=4.

DETAILED DESCRIPTION

The Genomewide Unbiased Identification of DSBs Evaluated by Sequencing (GUIDE-Seq) methods described herein provide highly sensitive, unbiased, and genome-wide methods for identifying the locations of engineered nuclease cleavage sites in living cells, e.g., cells in which the non-homologous end-joining (NHEJ) repair pathway is active. In some embodiments, the method relies on the capture of short double-stranded oligodeoxynucleotides (dsODNs) into nuclease-induced breaks (a process presumed to be mediated by the NHEJ pathway) and then the use of the inserted dsODN sequence to identify the sites of genomic insertion, e.g., using a PCR-based deep sequencing approach in which the inserted dsODN sequence is used to selectively amplify the sites of genomic insertion for high-throughput sequencing, or selectively pulling down genomic fragments including the inserted dsODNs using an attached tag such as biotin, e.g., using solution hybrid capture. Described herein is the development and validation of the GUIDE-Seq method in cultured human cells; the general approach described herein should work in all mammalian cells and in any cell type or organism in which the NHEJ pathway is active or presumed to be active.

The potential off-target sites identified by this initial sequencing process might also be analyzed for indel mutations characteristic of NHEJ repair in cells in which only the nuclease components are expressed. These experiments, which could be performed using amplification followed by deep sequencing, would provide additional confirmation and quantitation of the frequency of off-target mutations induced by each nuclease.

Double-Stranded Oligodeoxynucleotides (dsODNs)

In the methods described herein, a non-naturally occurring dsODN is expressed in the cells. In the present methods, both strands of the dsODN are orthogonal to the genome of the cell (i.e., are not present in or complementary to a sequence present in, i.e., have no more than 10%, 20%, 30%, 40%, or 50% identity to a sequence present in, the genome of the cell). The dsODNs can preferably be between 15 and 75 nts long, e.g., 15-50 nts, 50-75 nts, 30-35 nts, 60-65 nts, or 50-65 nts long, or between 15 and 50 nts long, e.g., 20-40 or 30-35, e.g., 32-34 nts long. Each strand of the dsODN should include a unique PCR priming sequence (i.e., the dsODN includes two PCR primer binding sites, one on each strand). In some embodiments, the dsODN includes a restriction enzyme recognition site, preferably a site that is relatively uncommon in the genome of the cell.

The dsODNs are preferably modified; preferably, the 5′ ends of the dsODN are phosphorylated; and also preferably, two phosphorothioate linkages are present on both 3′ ends and both 5′ ends. In preferred embodiments, the dsODN is blunt ended. In some embodiments, the dsODNs include a random variety of 1, 2, 3, 4 or more nucleotide overhangs on the 5′ or 3′ ends.

The dsODN can also include one or more additional modifications, e.g., as known in the art or described in PCT/US2011/060493. For example, in some embodiments, the dsODN is biotinylated. The biotinylated version of the GUIDE-seq dsODN tag is used as a substrate for integration into the sites of genomic DSBs. The biotin can be anywhere internal to the dsODN (e.g., a modified thymidine residue (Biotin-dT) or using biotin azide), but not on the 5′ or 3′ ends. As shown in Example 4, it is possible to integrate such an oligo efficiently. This provides an alternate method of recovering fragments that contain the GUIDE-seq dsODN tag. Whereas in some embodiments, these sequences are retrieved and identified by nested PCR, in this approach they are physically pulled down by using the biotin, e.g., by binding to streptavidin-coated magnetic beads, or using solution hybrid capture; see, e.g., Gnirke et al., Nature Biotechnology 27, 182-189 (2009). The primary advantage is retrieval of both flanking sequences, which reduces the dependence on mapping sequences to a reference genome to identify off-target cleavage sites.

Engineered Nucleases

There are four main classes of engineered nucleases: 1) meganucleases, 2) zinc-finger nucleases, 3) transcription activator effector-like nucleases (TALEN), and 4) Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) Cas RNA-guided nucleases (RGN). See, e.g., Gaj et al., Trends Biotechnol. 2013 July; 31(7):397-405. The nuclease can be transiently or stably expressed in the cell, using methods known in the art; typically, to obtain expression, a sequence encoding a protein is subcloned into an expression vector that contains a promoter to direct transcription. Suitable eukaryotic expression systems are well known in the art and described, e.g., in Sambrook et al., Molecular Cloning, A Laboratory Manual (4th ed. 2013); Kriegler, Gene Transfer and Expression: A Laboratory Manual (2006); and Current Protocols in Molecular Biology (Ausubel et al., eds., 2010). Transformation of eukaryotic and prokaryotic cells are performed according to standard techniques (see, e.g., the reference above and Morrison, 1977, J. Bacteriol. 132:349-351; Clark-Curtiss & Curtiss, Methods in Enzymology 101:347-362 (Wu et al., eds, 1983).

Homing Meganucleases

Meganucleases are sequence-specific endonucleases originating from a variety of organisms such as bacteria, yeast, algae and plant organelles. Endogenous meganucleases have recognition sites of 12 to 30 base pairs; customized DNA binding sites with 18 bp and 24 bp-long meganuclease recognition sites have been described, and either can be used in the present methods and constructs. See, e.g., Silva, G, et al., Current Gene Therapy, 11:11-27, (2011); Arnould et al., Journal of Molecular Biology, 355:443-58 (2006); Arnould et al., Protein Engineering Design & Selection, 24:27-31 (2011); and Stoddard, Q. Rev. Biophys. 38, 49 (2005); Grizot et al., Nucleic Acids Research, 38:2006-18 (2010).

CRISPR-Cas Nucleases

Recent work has demonstrated that clustered, regularly interspaced, short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems (Wiedenheft et al., Nature 482, 331-338 (2012); Horvath et al., Science 327, 167-170 (2010); Terns et al., Curr Opin Microbiol 14, 321-327 (2011)) can serve as the basis of a simple and highly efficient method for performing genome editing in bacteria, yeast and human cells, as well as in vivo in whole organisms such as fruit flies, zebrafish and mice (Wang et al., Cell 153, 910-918 (2013); Shen et al., Cell Res (2013); Dicarlo et al., Nucleic Acids Res (2013); Jiang et al., Nat Biotechnol 31, 233-239 (2013); Jinek et al., Elife 2, e00471 (2013); Hwang et al., Nat Biotechnol 31, 227-229 (2013); Cong et al., Science 339, 819-823 (2013); Mali et al., Science 339, 823-826 (2013c); Cho et al., Nat Biotechnol 31, 230-232 (2013); Gratz et al., Genetics 194(4):1029-35 (2013)). The Cas9 nuclease from S. pyogenes (hereafter simply Cas9) can be guided via simple base pair complementarity between 17-20 nucleotides of an engineered guide RNA (gRNA), e.g., a single guide RNA or crRNA/tracrRNA pair, and the complementary strand of a target genomic DNA sequence of interest that lies next to a protospacer adjacent motif (PAM), e.g., a PAM matching the sequence NGG or NAG (Shen et al., Cell Res (2013); Dicarlo et al., Nucleic Acids Res (2013); Jiang et al., Nat Biotechnol 31, 233-239 (2013); Jinek et al., Elife 2, e00471 (2013); Hwang et al., Nat Biotechnol 31, 227-229 (2013); Cong et al., Science 339, 819-823 (2013); Mali et al., Science 339, 823-826 (2013c); Cho et al., Nat Biotechnol 31, 230-232 (2013); Jinek et al., Science 337, 816-821 (2012)).

In some embodiments, the present system utilizes a wild type or variant Cas9 protein from S. pyogenes or Staphylococcus aureus, either as encoded in bacteria or codon-optimized for expression in mammalian cells. The guide RNA is expressed in the cell together with the Cas9. Either the guide RNA or the nuclease, or both, can be expressed transiently or stably in the cell.

TAL Effector Repeat Arrays

TAL effectors of plant pathogenic bacteria in the genus Xanthomonas play important roles in disease, or trigger defense, by binding host DNA and activating effector-specific host genes. Specificity depends on an effector-variable number of imperfect, typically ˜33-35 amino acid repeats. Polymorphisms are present primarily at repeat positions 12 and 13, which are referred to herein as the repeat variable-diresidue (RVD). The RVDs of TAL effectors correspond to the nucleotides in their target sites in a direct, linear fashion, one RVD to one nucleotide, with some degeneracy and no apparent context dependence. In some embodiments, the polymorphic region that grants nucleotide specificity may be expressed as a triresidue or triplet.

Each DNA binding repeat can include a RVD that determines recognition of a base pair in the target DNA sequence, wherein each DNA binding repeat is responsible for recognizing one base pair in the target DNA sequence. In some embodiments, the RVD can comprise one or more of: HA for recognizing C; ND for recognizing C; HI for recognizing C; HN for recognizing G; NA for recognizing G; SN for recognizing G or A; YG for recognizing T; and NK for recognizing and one or more of: HD for recognizing C; NG for recognizing T; NI for recognizing A; NN for recognizing G or A; NS for recognizing A or C or G or T; N* for recognizing C or T, wherein * represents a gap in the second position of the RVD; HG for recognizing T; H* for recognizing T, wherein * represents a gap in the second position of the RVD; and IG for recognizing T.

TALE proteins may be useful in research and biotechnology as targeted chimeric nucleases that can facilitate homologous recombination in genome engineering (e.g., to add or enhance traits useful for biofuels or biorenewables in plants). These proteins also may be useful as, for example, transcription factors, and especially for therapeutic applications requiring a very high level of specificity such as therapeutics against pathogens (e.g., viruses) as non-limiting examples.

Methods for generating engineered TALE arrays are known in the art, see, e.g., the fast ligation-based automatable solid-phase high-throughput (FLASH) system described in U.S. Ser. No. 61/610,212, and Reyon et al., Nature Biotechnology 30,460-465 (2012); as well as the methods described in Bogdanove & Voytas, Science 333, 1843-1846 (2011); Bogdanove et al., Curr Opin Plant Biol 13, 394-401 (2010); Scholze & Boch, J. Curr Opin Microbiol (2011); Boch et al., Science 326, 1509-1512 (2009); Moscou & Bogdanove, Science 326, 1501 (2009); Miller et al., Nat Biotechnol 29, 143-148 (2011); Morbitzer et al., T. Proc Natl Acad Sci USA 107, 21617-21622 (2010); Morbitzer et al., Nucleic Acids Res 39, 5790-5799 (2011); Zhang et al., Nat Biotechnol 29, 149-153 (2011); Geissler et al., PLoS ONE 6, e19509 (2011); Weber et al., PLoS ONE 6, e19722 (2011); Christian et al., Genetics 186, 757-761 (2010); Li et al., Nucleic Acids Res 39, 359-372 (2011); Mahfouz et al., Proc Natl Acad Sci USA 108, 2623-2628 (2011); Mussolino et al., Nucleic Acids Res (2011); Li et al., Nucleic Acids Res 39, 6315-6325 (2011); Cermak et al., Nucleic Acids Res 39, e82 (2011); Wood et al., Science 333, 307 (2011); Hockemeye et al. Nat Biotechnol 29, 731-734 (2011); Tesson et al., Nat Biotechnol 29, 695-696 (2011); Sander et al., Nat Biotechnol 29, 697-698 (2011); Huang et al., Nat Biotechnol 29, 699-700 (2011); and Zhang et al., Nat Biotechnol 29, 149-153 (2011); all of which are incorporated herein by reference in their entirety.

Zinc Fingers

Zinc finger proteins are DNA-binding proteins that contain one or more zinc fingers, independently folded zinc-containing mini-domains, the structure of which is well known in the art and defined in, for example, Miller et al., 1985, EMBO J., 4:1609; Berg, 1988, Proc. Natl. Acad. Sci. USA, 85:99; Lee et al., 1989, Science. 245:635; and Klug, 1993, Gene, 135:83. Crystal structures of the zinc finger protein Zif268 and its variants bound to DNA show a semi-conserved pattern of interactions, in which typically three amino acids from the alpha-helix of the zinc finger contact three adjacent base pairs or a “subsite” in the DNA (Pavletich et al., 1991, Science, 252:809; Elrod-Erickson et al., 1998, Structure, 6:451). Thus, the crystal structure of Zif268 suggested that zinc finger DNA-binding domains might function in a modular manner with a one-to-one interaction between a zinc finger and a three-base-pair “subsite” in the DNA sequence. In naturally occurring zinc finger transcription factors, multiple zinc fingers are typically linked together in a tandem array to achieve sequence-specific recognition of a contiguous DNA sequence (Klug, 1993, Gene 135:83).

Multiple studies have shown that it is possible to artificially engineer the DNA binding characteristics of individual zinc fingers by randomizing the amino acids at the alpha-helical positions involved in DNA binding and using selection methodologies such as phage display to identify desired variants capable of binding to DNA target sites of interest (Rebar et al., 1994, Science, 263:671; Choo et al., 1994 Proc. Natl. Acad. Sci. USA, 91:11163; Jamieson et al., 1994, Biochemistry 33:5689; Wu et al., 1995 Proc. Natl. Acad. Sci. USA, 92: 344). Such recombinant zinc finger proteins can be fused to functional domains, such as transcriptional activators, transcriptional repressors, methylation domains, and nucleases to regulate gene expression, alter DNA methylation, and introduce targeted alterations into genomes of model organisms, plants, and human cells (Carroll, 2008, Gene Ther., 15:1463-68; Cathomen, 2008, Mol. Ther., 16:1200-07; Wu et al., 2007, Cell. Mol. Life Sci., 64:2933-44).

One existing method for engineering zinc finger arrays, known as “modular assembly,” advocates the simple joining together of pre-selected zinc finger modules into arrays (Segal et al., 2003, Biochemistry, 42:2137-48; Beerli et al., 2002, Nat. Biotechnol., 20:135-141; Mandell et al., 2006, Nucleic Acids Res., 34:W516-523; Carroll et al., 2006, Nat. Protoc. 1:1329-41; Liu et al., 2002, J. Biol. Chem., 277:3850-56; Bae et al., 2003, Nat. Biotechnol., 21:275-280; Wright et al., 2006, Nat. Protoc., 1:1637-52). Although straightforward enough to be practiced by any researcher, recent reports have demonstrated a high failure rate for this method, particularly in the context of zinc finger nucleases (Ramirez et al., 2008, Nat. Methods, 5:374-375; Kim et al., 2009, Genome Res. 19:1279-88), a limitation that typically necessitates the construction and cell-based testing of very large numbers of zinc finger proteins for any given target gene (Kim et al., 2009, Genome Res. 19:1279-88).

Combinatorial selection-based methods that identify zinc finger arrays from randomized libraries have been shown to have higher success rates than modular assembly (Maeder et al., 2008, Mol. Cell, 31:294-301; Joung et al., 2010, Nat. Methods, 7:91-92; Isalan et al., 2001, Nat. Biotechnol., 19:656-660). In preferred embodiments, the zinc finger arrays are described in, or are generated as described in, WO 2011/017293 and WO 2004/099366. Additional suitable zinc finger DBDs are described in U.S. Pat. Nos. 6,511,808, 6,013,453, 6,007,988, and 6,503,717 and U.S. patent application 2002/0160940.

Cells

The methods described herein can be used in any cell that is capable of repairing a DSB in genomic DNA. The two major DSB repair pathways in eukaryotic cells are Homologous recombination (HR) and Non-homologous end joining (NHEJ). Preferably, the methods are performed in cells capable of NHEJ. Methods for detecting NHEJ activity are known in the art; for a review of the NHEJ canonical and alternative pathways, see Liu et al., Nucleic Acids Res. Jun. 1, 2014; 42(10):6106-6127.

Sequencing

As used herein, “sequencing” includes any method of determining the sequence of a nucleic acid. Any method of sequencing can be used in the present methods, including chain terminator (Sanger) sequencing and dye terminator sequencing. In preferred embodiments, Next Generation Sequencing (NGS), a high-throughput sequencing technology that performs thousands or millions of sequencing reactions in parallel, is used. Although the different NGS platforms use varying assay chemistries, they all generate sequence data from a large number of sequencing reactions run simultaneously on a large number of templates. Typically, the sequence data is collected using a scanner, and then assembled and analyzed bioinformatically. Thus, the sequencing reactions are performed, read, assembled, and analyzed in parallel; see, e.g., US 20140162897, as well as Voelkerding et al., Clinical Chem., 55: 641-658, 2009; and MacLean et al., Nature Rev. Microbiol., 7: 287-296 (2009). Some NGS methods require template amplification and some that do not. Amplification-requiring methods include pyrosequencing (see, e.g., U.S. Pat. Nos. 6,210,89 and 6,258,568; commercialized by Roche); the Solexa/Illumina platform (see, e.g., U.S. Pat. Nos. 6,833,246, 7,115,400, and 6,969,488); and the Supported Oligonucleotide Ligation and Detection (SOLiD) platform (Applied Biosystems; see, e.g., U.S. Pat. Nos. 5,912,148 and 6,130,073). Methods that do not require amplification, e.g., single-molecule sequencing methods, include nanopore sequencing, HeliScope (U.S. Pat. Nos. 7,169,560; 7,282,337; 7,482,120; 7,501,245; 6,818,395; 6,911,345; and 7,501,245); real-time sequencing by synthesis (see, e.g., U.S. Pat. No. 7,329,492); single molecule real time (SMRT) DNA sequencing methods using zero-mode waveguides (ZMWs); and other methods, including those described in U.S. Pat. Nos. 7,170,050; 7,302,146; 7,313,308; and 7,476,503). See, e.g., US 20130274147; US20140038831; Metzker, Nat Rev Genet 11(1): 31-46 (2010).

Alternatively, hybridization-based sequence methods or other high-throughput methods can also be used, e.g., microarray analysis, NANOSTRING, ILLUMINA, or other sequencing platforms.

EXAMPLES

The invention is further described in the following examples, which do not limit the scope of the invention described in the claims.

Example 1

In initial experiments, the process of integrating a dsODN cassette into nuclease-induced double-stranded breaks (DSBs) was optimized. Previously published experiments had demonstrated that dsODNs bearing two phosphorothiorate linkage modifications at their 5′ ends could be captured into a zinc finger nuclease (ZFN)-induced DSB in mammalian cells (Orlando et al., Nucleic Acids Res. 2010 August; 38(15):e152). However, to use the capture of such ssODNs to identify even very low frequency DSBs, the characteristics of the dsODN were optimized to improve its rate of capture into such breaks. Initial efforts were focused on capture of the dsODN into DSBs induced by the Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) RNA-guided nuclease Cas9 from Streptococcus pyogenes. Cas9 has been reported to induce DSBs with blunt ends and therefore dsODN variants were designed that were blunt-ended. Optimization experiments showed that the phosphorylation of both 5′ ends and the introduction of two phosphorothiorate linkages on both 3′ ends (in addition to the ones on the 5′ ends) led to substantially increased rate of capture of a dsODN into a Cas9-induced DSB (FIGS. 1A-B). Sanger sequencing verified the successful capture of the dsODN into this particular DSB (FIGS. 2A-B).

Having established that dsODNs can be efficiently integrated into Cas9-induced DSBs, the next experiments sought to determine whether next-generation deep sequencing methods could be used to capture, amplify and identify the sites of dsODN integrations in the genomes of mammalian cells. To do this, a 34 bp dsODN was utilized that contains two PCR primer binding sites (one on each strand); these sequences were chosen because they are each orthogonal to the human genome.

The sequence of the dsODN used is provided in Table 1:

TABLE 1 SEQ ID Strand Sequence (5′ to 3′) NO: FWD /5Phos/ 1 G*T*TTAATTGAGTTGICATATGTTAATAACGGT*A*T REV /5Phos/ 2 A*T*ACCGTTATTAACATATGACAACTCAATTAA*A*C /5Phos/ denotes 5′ phosphorylation. *denotes phosphorothioate linkage between adjacent nucleotides.

This dsODN was transfected into human U2OS cells together with plasmids encoding Cas9 and one of four different target-specific gRNAs, each targeted to a different endogenous human gene sequence (EMX1 and VEGFA sites 1, 2, and 3). These four particular gRNAs were chosen because bona fide off-target sites had been previously identified for each of them (Fu et al., Nat Biotechnol. 2013; Table 1). The transfections were performed as follows: dsODN is annealed in STE (100 mM TrisHcl, 500 mM NaCl, 10 mM EDTA) at a concentration of 100 uM each. For U2OS cells, 500 ng of Cas9 expression plasmid, 250 ng gRNA expression plasmid, and 100 pmol of dsODN were used to nucleofect 2E5 cells with solution SE and program DN-100.

Genomic DNA was harvested three days post-transfection (Agencourt AMPURE XP automated PCR purification system) and a PCR-based restriction fragment length polymorphisms (RFLP) assay was used to verify that the dsODN had been efficiently integrated into the on-target site in these cells based on the presence of a restriction site encoded in the dsODN.

To comprehensively identify the locations of dsODN integration in the genomes of the transfected cells, a PCR-based method was used that selectively amplifies these insertion sites and also enables them to be sequenced using next-generation sequencing technology. A general overview of the strategy is shown in FIG. 3. Genomic DNA was sheared with a Covaris Adaptive Focused Acoustic (AFA) focused ultrasonicator to a mean length of 500 bp. Sheared gDNA was end-repaired (Enzymatics), A-tailed (Enzymatics), and a half-functional sequencing adapter (US 20130303461) was ligated (Enzymatics) to the ends of the sheared DNA. Solid Phase Reversible Immobilization (SPRI) magnetic bead cleanup was used to clean up each of these enzymatic steps (Agencourt XP).

DNA fragments bearing the dsODN sequence were then amplified using a primer specific to the dsODN together with a primer that anneals to the sequencing adapter. Because there are two potential priming sites within the dsODN (one on each strand as noted above), two independent PCR reactions were performed to selectively amplify the desired sequences as follows.

Two rounds of nested PCR were performed to generate a targeted sequencing library. The first round of PCR was performed using a primer complementary to the integration dsODN (primer A) and a primer complementary to the universal adapter (primer B). The second round of PCR was performed using a 3′ nested primer complementary to primer A (primer C), a 3′ nested primer complementary to primer B (primer D), and a primer that was complementary to primer D (primer E) that added a flow-cell binding sequence and random molecular index to make a ‘complete’ molecule that was ready for sequencing. SPRI magnetic beads were used to clean up each round of PCR. (Agencourt AMPURE XP automated PCR purification system).

The amplification of dsODN-containing genomic sequences by this approach neither depends on nor is biased by flanking sequence adjacent to the insertion point because the sequencing adapter is ligated to breaks induced by random sharing of genomic DNA. An additional round of PCR was performed to add next-generation sequencing adapter sequences and an indexing barcode on the end closest to the dsODN, resulting in a library of fragments that is ready for next-generation sequencing. This general method is referred to herein as GUIDE-Seq, for Genomewide Unbiased Identification of DSBs Evaluated by Sequencing.

Deep sequencing of the libraries constructed using GUIDE-Seq revealed a wide range of genomic loci into which the dsODN had become inserted in the presence of each of the four co-expressed gRNA/Cas9 nucleases. In analyzing the raw deep sequencing data, it was reasoned that bona fide sites of insertion could be identified as genomic loci that were covered by at least one read in both orientations. Reads in both directions were possible both because the dsODN could insert in either orientation and because amplifications were performed using primers specific for either one or the other strand in the dsODN sequence. A total of 465 genomic loci were identified that met this criterion for the four gRNAs examined. For 36% of these 465 loci a sequence within 25 bps of the insertion point was also identified that was similar to the on-target site of the gRNA used and bearing as many as six mismatches relative to the on-target site (FIGS. 4A-E). This method also successfully discovered all previously known bona fide off-target sites for all four gRNAs examined here (all of the previously known off-target sites shown in FIG. 4 are also present in Table 1 from Fu et al., Nat Biotechnol. 2013) as well as many additional previously unknown off-target sites.

Example 2

Customizable CRISPR-Cas RNA-guided nucleases (RGNs) are robust, customizable genome-editing reagents with a broad range of research and potential clinical applications^(1, 2); however, therapeutic use of RGNs in humans will require full knowledge of their off-target effects to minimize the risk of deleterious outcomes. DNA cleavage by S. pyogenes Cas9 nuclease is directed by a programmable ˜100 nt guide RNA (gRNA).³, Targeting is mediated by 17-20 nts at the gRNA 5′-end, which are complementary to a “protospacer” DNA site that lies next to a protospacer adjacent motif (PAM) of the form 5′-NGG. Repair of Cas9-induced DNA double-stranded breaks (DSBs) within the protospacer by non-homologous end-joining (NHEJ) can induce variable-length insertion/deletion mutations (indels). Our group and others have previously shown that unintended RGN-induced indels can occur at off-target cleavage sites that differ by as many as five positions within the protospacer or that harbor alternative PAM sequences⁴⁻⁷. Chromosomal translocations can result from joining of on- and off-target RGN-induced cleavage events⁸⁻¹¹. For clinical applications, identification of even low frequency alterations will be critically important because ex vivo and in vivo therapeutic strategies using RGNs are expected to require the modification of very large cell populations. The induction of oncogenic transformation in even a rare subset of cell clones (e.g., inactivating mutations of a tumor suppressor gene or formation of a tumorigenic chromosomal translocation) is of particular concern because such an alteration could lead to unfavorable clinical outcomes.

The comprehensive identification of indels or higher-order genomic rearrangements that can occur anywhere in the genome is a challenge that is not easily addressed, and unfortunately sensitive methods for unbiased, genome-wide identification of RGN-induced off-target mutations in living cells have not yet been described^(12, 13). Whole genome re-sequencing has been used to attempt to identify RGN off-target alterations in edited single cell clones^(14, 15) but the high cost of sequencing very large numbers of genomes makes this method impractical for finding low frequency events in cell populations¹². We and others have used focused deep sequencing to identify indel mutations at potential off-target sites identified either by sequence similarity to the on-target site^(4, 5) or by in vitro selection from partially degenerate binding site libraries⁶. However, these approaches make assumptions about the nature of off-target sequences and therefore may miss other mutation sites elsewhere in the genome. ChIP-Seq has also been used to identify off-target binding sites for gRNAs complexed with catalytically dead Cas9 (dCas9), but the majority of published work suggests that very few, if any, of these sites represent off-target sites of cleavage by active Cas9 nuclease¹⁶⁻¹⁹.

Here we describe the development of a novel method for Genome-wide Unbiased Identification of DSBs Evaluated by Sequencing (GUIDE-Seq), which enabled us to generate the first global specificity landscapes for ten different RGNs in living human cells. These profiles revealed that the total number of off-target DSBs varied widely for individual RGNs and suggested that broad conclusions about the specificity of RGNs from S. pyogenes or other species should be based on large surveys and not on just small numbers of gRNAs. Our findings also expanded the range and nature of sequences at which off-target effects can occur. Direct comparisons demonstrated that GUIDE-Seq substantially outperformed two widely used computational approaches and a ChIP-Seq method for identifying RGN off-target sites. Unexpectedly, GUIDE-Seq also identified RGN-independent DNA breakpoint hotspots that can participate together with RGN-induced DSBs in higher-order genomic alterations such as translocations. Lastly, we show in direct comparisons that truncating the complementarity region of gRNAs greatly improved their genome-wide off-target DSB profiles, demonstrating the utility of GUIDE-Seq for evaluating advances designed to improve RGN specificities. The experiments outlined here provide the most rigorous strategy described to date for evaluating the specificities of RGNs, as well as of any improvements to the platform, that may be considered for therapeutic use.

Methods

The following materials and methods were used in this Example.

Human Cell Culture and Transfection

U2OS and HEK293 cells were cultured in Advanced DMEM (Life Technologies) supplemented with 10% FBS, 2 mM GLUTAMAX media supplement (Life Technologies), and penicillin/streptomycin at 37° C. with 5% CO₂. U2OS cells (program DN-100) and HEK293 cells (program CM-137) were transfected in 20 μl Solution SE on a Lonza NUCLEOFECTOR 4-D transfection system according to the manufacturer's instructions. dsODN integration rates were assessed by restriction fragment length polymorphism (RFLP) assay using NdeI. Cleavage products were run and quantified by a QIAXCEL capillary electrophoresis instrument (Qiagen) as previously described (Tsai et al., Nat. Biotechnol 32, 569-576 (2014)).

Isolation and Preparation of Genomic DNA for GUIDE-Seq

Genomic DNA was isolated using solid-phase reversible immobilization magnetic beads (Agencourt DNAdvance), sheared with a Covaris S200 sonicator to an average length of 500 bp, end-repaired, A-tailed, and ligated to half-functional adapters, incorporating a 8-nt random molecular index. Two rounds of nested anchored PCR, with primers complementary to the oligo tag, were used for target enrichment. Full details of the exemplary GUIDE-Seq protocol can be found herein.

Processing and Consolidation of Sequencing Reads

Reads that share the same six first bases of sequence as well as identical 8-nt molecular indexes were binned together because they are assumed to originate from the same original pre-PCR template fragment. These reads were consolidated into a single consensus read by selecting the majority base at each position. A no-call (N) base was assigned in situations with greater than 10% discordant reads. The base quality score was taken to be the highest among the pre-consolidation reads. Consolidated reads were mapped to human genome reference (GrCh37) using BWA-MEM (Li and Durbin, Bioinformatics 26, 589-595 (2010)).

Identification of Off-Target Cleavage Sites

Start mapping positions for reads with mapping quality ≧50 were tabulated, and regions with nearby start mapping positions were grouped using a 10-bp sliding window. Genomic windows harboring integrated dsODNs were identified by one of the following criteria: 1) two or more unique molecular-indexed reads mapping to opposite strands in the reference sequence or 2) two or more unique molecular-indexed reads amplified by forward and reverse primers. 25 bp of reference sequence flanking both sides of the inferred breakpoints were aligned to the intended target site and RGN off-target sites with eight or fewer mismatches from the intended target sequence were called. SNPs and indels were called in these positions by a custom bin-consensus variant-calling algorithm based on molecular index and SAMtools, and off-target sequences that differed from the reference sequence were replaced with the corresponding cell-specific sequence.

AMP-Based Sequencing

For AMP validation of GUIDE-Seq detected DSBs, primers were designed to regions flanking inferred double-stranded breakpoints as described previously (Zheng, Z. et al. Anchored multiplex PCR for targeted next-generation sequencing. Nat Med 2014 November 10. doi: 10.1038/nm.3729 (2014)), with the addition of an 8-nt molecular molecular index. Where possible, we designed two primers to flank each DSB.

Analysis of AMP Validation Data

Reads with average quality scores >30 were analyzed for insertions, deletions, and integrations that overlapped with the GUIDE-Seq inferred DSB positions using Python. 1-bp indels were included only if they were within 1-bp of the predicted DSB site to minimize the introduction of noise from PCR or sequencing error. Integration and indel frequencies were calculated on the basis of consolidated molecular indexed reads.

Structural Variation

Translocations, large deletions, and inversions were identified using a custom algorithm based on split BWA-MEM alignments. Candidate fusion breakpoints within 50 bases on the same chromosome were grouped to accommodate potential resection around the Cas9 cleavage site. A fusion event was called with at least 3 uniquely mapped split reads, a parameter also used by the segemehl tool (Hoffmann, Genome biology, 2014)). Mapping strandedness was maintained for identification of reciprocal fusions between two involving DSBs, and for determining deletion or inversion. Fusions involved DSBs within lkb chromosomal positions were discarded for consideration of large indels caused by single Cas9 cleavage. Remaining fusion DSBs were classified in four categories: ‘on-target’, ‘off-target’, or ‘background’ based on GUIDE-seq or, else, ‘other’.

Comparison of Sites Detected by GUIDE-Seq and ChIP-Seq and in Silico Predictions

We used the MIT CRISPR Design Tool to identify potential off-target sites for all ten RGNs. This tool assigns each potential off-target site a corresponding percentile. We then grouped these percentiles into quintiles for visualization purposes. Because the E-CRISP tool does not rank off-targets, we simply found the GUIDE-seq off-targets that were correctly predicted by E-CRISP. For both of these GUIDE-Seq vs. in silico predictions, we also split the GUIDE-Seq results that were not predicted by the in silico method into off-targets that have mismatch numbers within the range of the MIT tool (maximum of 4) and E-CRISPR (maximum of 3), and those with mismatch numbers greater than the threshold of these prediction tools. In comparing the GUIDE-Seq off-targets with ChIP-Seq predictions, the same technique was used to find the GUIDE-Seq off-targets correctly predicted by the ChIP-Seq. For each of these comparisons, every grouping that was made was subdivided by off-target mismatch number to better characterize the properties of correctly and incorrectly predicted RGN off-targets.

Analysis of Impact of Mismatches, DNA Accessibility and Local PAM Density on Off-Target Cleavage Rate

We assessed the impact of mismatch position, mismatch type and DNA accessibility on specificity using linear regression models fit to estimated cleavage rates at potential off-target sites with four or less mismatches. Mismatch position covariates were defined as the number of mismatched bases within each of five non-overlapping 4-bp windows upstream of the PAM. Mismatch type covariates were defined as i) the number mismatches resulting in wobble pairing (target T replaced by C, target G replaced by A), ii) the number of mismatches resulting in a non-wobble purine-pyrimidine base-pairing (target C replaced by T, target A replaced by G), and iii) the number as mismatches resulting in purine-purine or pyrimidine-pyrimidine pairings.

Each of the three factors was used in separate model as a predictor of relative cleavage rates, estimated by log 2(1+GUIDE-Seq read count). The effect size estimates were adjusted for inter-target site variability. The proportion of intra-site cleavage rate variability explained by each factor was assessed by the partial eta-squared statistic based on the regression sums of squares (SS): η² _(p)=SS_(factor)/(SS_(factor)+SS_(error)). In addition to the single-factor models, we also fit a combined linear regression model including all three factors, expression level, and PAM density in a 1-kb window to assess their independent contribution to off-target cleavage probability.

Exemplary Reagents and Equipment for Guide-seq Library Preparation Store at Room Temperature

Item Vendor Covaris S220 microTube, Covaris Ethanol, 200-proof (100%) Sigma Aldrich MICROAMP Optical 96-well Plates Applied Biosystems Nuclease-free H₂O Promega QUBIT fluorometric quantitation Assay Tubes, Invitrogen 500 tubes/pack QUBIT fluorometric quantitation dsDNA BR Invitrogen Kit-500 Assays TMAC Buffer, 5M Sigma Aldrich Tetramethylammonium Chloride 1X TE Buffer/10 mM Tris-HCl, pH 8.0 Invitrogen UltraPure 0.5M EDTA, pH 8.0 (Gibco) Life Technologies (4 × 100 mL)

Store at 4° C.

Item Vendor Agencourt AMPURE XP Beads-60 mL Beckman Coulter

Store at −20° C.

Item Catalog # 25 mM dNTP Solution Mix Enzymatics, Inc. Slow ligation buffer Enzymatics, Inc. End-repair mix (low concentration) Enzymatics, Inc. T4 DNA Ligase Enzymatics, Inc. 10X T4 DNA Ligase Buffer (Slow Ligation Buffer) Platinum ® Taq DNA Polymerase Life Technologies 10X PCR Buffer (no MgCl₂) 50 mM MgCl₂ qPCR Illumina Library Quantification Kits KAPA Biosystems, Inc.

Equipment

96-well Plate Magnetic Stand Invitrogen QUBIT Fluorometer 2.0 Life Technologies Covaris S-2 Focused Ultra-sonicator ™ Instrument Covaris Tabletop centrifuge Thermo Scientific Tabletop vortexer Thermo Scientific Thermocycler Eppendorf MISEQ genome sequencer Illumina

Exemplary Protocol for GUIDE-seq Library Preparation Y-Adapter Preparation

The Y-adapter is made by annealing the MISEQ genome sequencer common oligo with each of the sample barcode adapters (A01 to A16, see Table 4). The adapters also contain 8-mer NNWNNWNN (N=A, C, T, or G; W=A or T) molecular indexes.

1X TE Buffer  80.0 μL A## (100 μM)  10.0 μL MISEQ genome sequencer Common Adapter_MI  10.0 μL (100 μM) Total 100.0 μL

Annealing program: 95° C. for 1 s; 60° C. for 1 s; slow ramp down (approximately −2° C./min) to 4° C.; hold at 4° C. Store in −20° C.

Input Quantification and Shearing

1. dsDNA is quantified by QUBIT fluorometric quantitation and 400 ng is brought to a final volume of 120 ul using 1×TE Buffer. 2. Each sample is sheared to an average length of 500 bp according to the standard operating protocol for the Covaris S2. 3. A cleanup with 120 ul of AMPURE XP SPRI PCR purification beads (1× ratio) is performed according to manufacturer protocol, and eluted in 15 ul of 1×TE Buffer.

End Repair, A-Tailing and Ligation End Repair

4. To a 200 μL PCR tube or well in a 96-well plate, add the following (per reaction):

Nuclease-free H₂O  0.5 μL dNTP mix, 5 mM  1.0 μL SLOW Ligation Buffer, 10X  2.5 μL End-repair mix (low concentration)  2.0 μL Buffer for Taq Polymerase, 10X (Mg2 + free)  2.0 μL Taq Polymerase (non-hot start)  0.5 μL Total  8.5 μL +DNA sample (from previous step) 14.0 μL Total 22.5 μL

End Repair Thermocycler Program: 12° C. for 15 min, 37° C. for 15 min; 72° C. for 15 min; hold at 4° C.

Adapter Ligation

5. To the sample reaction tube or well, add the following reagents in order (mix by pipetting):

Annealed Y adapter_MI (10 μM)  1.0 μL T4 DNA Ligase  2.0 μL +DNA sample (from previous step) 22.5 μL Total 25.5 μL

Adapter Ligation Thermocycler Program: 16° C. for 30 min, 22° C. for 30 min, hold at 4° C.

6. 0.9×SPRI clean (22.95 ul AMPURE XP PCR purification beads), elute in 12 uL of 1×TE buffer.

PCRs PCR 1 (Oligo Tag Primer [Discovery] or Large Primer Pool [Deep-Sequencing Validation])

7. Prepare the following master mix:

Nuclease-free H₂O 11.9 μL Buffer for Taq Polymerase, 10X (MgCl₂ free)  3.0 μL dNTP mix, 10 mM  0.6 μL MgCl₂, 50 mM  1.2 μL Platinum Taq polymerase, 5 U/μL  0.3 μL GSP1 Primer (10 uM)/Primer Pool (*)  1.0 μL* TMAC (0.5M)  1.5 μL P5_1, 10 μM  0.5 μL Total 20.0 μL +DNA sample (from Step 6) 10.0 μL Total 30.0 μL *For Discovery, make separate master mixes for +/(sense) and −/(antisense) reactions, and proceed with separate PCR reactions. *For deep-sequencing validation, one master mix can be made. Primer Pool should be normalized to a total amount of 30 pmol in the 30 ul reaction.

Discovery Thermocycler Program (touchdown):

-   -   95° C. for 5 min,     -   15 cycles of [95° C. for 30 s, 70° C. (−1° C./cycle) for 2 min,         72° C. for 30 s],     -   10 cycles of [95° C. for 30 s, 55° C. for 1 min, 72° C. for 30         s],     -   72° C. for 5 min,     -   4° C. hold

Validation Thermocycler Program:

-   -   95° C. for 5 min,     -   14 cycles of [95° C. for 30 s, 20% ramping down to 65° C.,         65° C. for 5 min],     -   72° C. for 5 min,     -   4° C. hold         8. 1.2×SPRI clean (36.0 uL), elute in 15 ul of 1×TE Buffer.

PCR 2 (Oligo Tag Primer [Discovery] or Large Primer Pool [Deep-Sequencing Validation])

9. Prepare the following master mix:

Nuclease-free H₂O  5.4 μL Buffer for Taq Polymerase, 10X (Mg²⁺ free)  3.0 μL dNTP mix, 10 mM  0.6 μL MgCl₂, 50 mM  1.2 μL Platinum Taq polymerase, 5 U/μl  0.3 μL GSP2 Primer (10 uM)/Primer Pool (*)  1.0 μL TMAC (0.5M)  1.5 μL P5_2, 10 μM  0.5 μL Total 13.5 μL +P7_# (10 uM)*  1.5 μL +DNA sample with beads (from Step 8) 15.0 μL Total 30.0 μL Primer concentrations should follow the specifications described in PCR1 * For the P7_#, at least 4 should be used in one sequencing run for good image registration on Illumina sequencer (e.g. P701-P704 or P705-P708)

-   -   Discovery Thermocycler Program (touchdown):         -   same as for PCR1     -   Validation Thermocycler Program:         -   same as for PCR1             10. 0.7×SPRI clean (21.0 uL), elute in 30 ul of 1×TE Buffer.             Library Quantification by qPCR and Sequencing

qPCR Quantification

11. Quantitate library using Kapa Biosystems kit for Illumina Library Quantification kit, according to manufacturer instruction.

Normalization and Sequencing

12. Using the mean quantity estimate of number of molecules per uL given by the qPCR run for each sample, proceed to normalize the total set of libraries to 1.2×10̂10 molecules, divided by the number of libraries to be pooled together for sequencing. This will give a by molecule input for each sample, and also a by volume input for each sample.

After pooling, dry down the library with a VACUFUGE vacuum concentrator to a final volume of 10 uL for sequencing.

Denature the library and load onto the MISEQ genome sequencer according to Illumina's standard protocol for sequencing with an Illumina MISEQ genome sequencer Reagent Kit V2-300 cycle (2×150 bp paired end), except:

-   -   1) Add 3 ul of 100 μM custom sequencing primer Index 1 to MISEQ         genome sequencer Reagent cartridge position 13 (Index Primer         Mix). Add 3 ul of 100 μM custom sequencing primer Read 2 to         MISEQ genome sequencer Reagent cartridge position 14 (Read 2         Primer Mix).     -   2) Sequence with the following number of cycles “151|8|16|151”         with the paired-end Nextera sequencing protocol.         Submit sequencing data in either bcl or fastq format to relevant         pipelines for downstream bioinformatics analysis.

TABLE 3 Common Primers Needed for GUIDE-Seq SEQ ID Sequence (5′ → 3′) NO: P7 Adapters P701 CAAGCAGAAGACGGCATACGAGATTCGCCTTAGTGACTGGAGTCCTCTCTATGG  3 GCAGTCGGTGA P702 CAAGCAGAAGACGGCATACGAGATCTAGTACGGTGACTGGAGTCCTCTCTATGG  4 GCAGTCGGTGA P703 CAAGCAGAAGACGGCATACGAGATTTCTGCCTGTGACTGGAGTCCTCTCTATGG  5 GCAGTCGGTGA P704 CAAGCAGAAGACGGCATACGAGATGCTCAGGAGTGACTGGAGTCCTCTCTATGG  6 GCAGTCGGTGA P705 CAAGCAGAAGACGGCATACGAGATAGGAGTCCGTGACTGGAGTCCTCTCTATGG  7 GCAGTCGGTGA P706 CAAGCAGAAGACGGCATACGAGATCATGCCTAGTGACTGGAGTCCTCTCTATGG  8 GCAGTCGGTGA P707 CAAGCAGAAGACGGCATACGAGATGTAGAGAGGTGACTGGAGTCCTCTCTATGG  9 GCAGTCGGTGA P708 CAAGCAGAAGACGGCATACGAGATCCTCTCTGGTGACTGGAGTCCTCTCTATGG 10 GCAGTCGGTGA P5 Adapters P5_1 AATGATACGGCGACCACCGAGATCTA 11 P5_2 AATGATACGGCGACCACCGAGATCTACAC 12 Custom Sequencing Primers Index1 ATCACCGACTGCCCATAGAGAGGACTCCAGTCAC 13 Read2 GTGACTGGAGTCCTCTCTATGGGCAGTCGGTGAT 14 IIlumina Y- adapters  1-16 (with Molecular Index tag NNWNNWN N) MISEQ [Phos]GATCGGAAGAGC*C*A 15 Common Adapter A01 AATGATACGGCGACCACCGAGATCTACACTAGATCGCNNWNNWNNACACTCTT 16 TCCCTACACGACGCTCTTCCGATC A02 AATGATACGGCGACCACCGAGATCTACACCTCTCTATNNWNNWNNACACTCTTT 17 CCCTACACGACGCTCTTCCGATC*T A03 AATGATACGGCGACCACCGAGATCTACACTATCCTCTNNWNNWNNACACTCTTT 18 CCCTACACGACGCTCTTCCGATC*T A04 AATGATACGGCGACCACCGAGATCTACACAGAGTAGANNWNNWNNACACTCT 19 TTCCCTACACGACGCTCTTCCGATC*T A05 AATGATACGGCGACCACCGAGATCTACACGTAAGGAGNNWNNWNNACACTCT 20 TTCCCTACACGACGCTCTTCCGATC*T A06 AATGATACGGCGACCACCGAGATCTACACACTGCATANNWNNWNNACACTCTT 21 TCCCTACACGACGCTCTTCCGATC*T A07 AATGATACGGCGACCACCGAGATCTACACAAGGAGTANNWNNWNNACACTCT 22 TTCCCTACACGACGCTCTTCCGATC*T A08 AATGATACGGCGACCACCGAGATCTACACCTAAGCCTNNWNNWNNACACTCTT 23 TCCCTACACGACGCTCTTCCGATC*T A09 AATGATACGGCGACCACCGAGATCTACACGACATTGTNNWNNWNNACACTCTT 24 TCCCTACACGACGCTCTTCCGATC*T A10 AATGATACGGCGACCACCGAGATCTACACACTGATGGNNWNNWNNACACTCTT 25 TCCCTACACGACGCTCTTCCGATC*T A11 AATGATACGGCGACCACCGAGATCTACACGTACCTAGNNWNNWNNACACTCTT 26 TCCCTACACGACGCTCTTCCGATC*T A12 AATGATACGGCGACCACCGAGATCTACACCAGAGCTANNWNNWNNACACTCTT 27 TCCCTACACGACGCTCTTCCGATC*T A13 AATGATACGGCGACCACCGAGATCTACACCATAGTGANNWNNWNNACACTCTT 28 TCCCTACACGACGCTCTTCCGATC*T A14 AATGATACGGCGACCACCGAGATCTACACTACCTAGTNNWNNWNNACACTCTT 29 TCCCTACACGACGCTCTTCCGATC*T A15 AATGATACGGCGACCACCGAGATCTACACCGCGATATNNWNNWNNACACTCTT 30 TCCCTACACGACGCTCTTCCGATC*T A16 AATGATACGGCGACCACCGAGATCTACACTGGATTGTNNWNNWNNACACTCTT 31 TCCCTACACGACGCTCTTCCGATC*T Strand/ Primer Name Sequence (5′ → 3′) Direction Nuclease_off GGATCTCGACGCTCTCCCTATACCGTTATTAACATATGACA + 32 _+_GSP1 Nuclease_off GGATCTCGACGCTCTCCCTGTTTAATTGAGTTGTCATATGTTAATAA − 33 _−_GSP1 C Nuclease_off CCTCTCTATGGGCAGTCGGTGATACATATGACAACTCAATTAAAC + 34 _+_GSP2 Nuclease_off CCTCTCTATGGGCAGTCGGTGATTTGAGTTGTCATATGTTAATAAC − 35 _−_GSP2 GGTA *Indicates a Phosphorothioate Bond Modification

Results

Overview of Exemplary GUIDE-Seq Method

In some embodiments, GUIDE-Seq consists of two stages (FIG. 5B): In Stage I, DSBs in the genomes of living human cells are tagged by integration of a blunt double-stranded oligodeoxynucleotide (dsODN) at these breaks. In Stage II, dsODN integration sites in genomic DNA are precisely mapped at the nucleotide level using unbiased amplification and next-generation sequencing.

For Stage I, we optimized conditions to integrate a blunt, 5′ phosphorylated dsODN into RGN-induced DSBs in human cells. In initial experiments, we failed to observe integration of such dsODNs into RGN-induced DSBs. Using dsODNs bearing two phosphothiorate linkages at the 5′ ends of both DNA strands designed to stabilize the oligos in cells²⁰, we observed only modest detectable integration frequencies (FIG. 5B). However, addition of phosphothiorate linkages at the 3′ ends of both strands led to robust integration efficiencies (FIG. 5B). These rates of integration were only two- to three-fold lower than the frequencies of indels induced by RGNs alone at these sites (i.e., in the absence of the dsODN).

For Stage II, we developed a novel strategy that allowed us to selectively amplify and sequence, in an unbiased fashion, only those fragments bearing an integrated dsODN (FIG. 5A). We accomplished this by first ligating “single-tail” next-generation sequencing adapters to randomly sheared genomic DNA from cells into which dsODN and plasmids encoding RGN components had been transfected. We then performed a series of PCR reactions initiated by one primer that specifically anneals to the dsODN and another that anneals to the sequencing adapter (FIG. 5A and FIG. 12). Because the sequencing adapter is only single-tailed, this enables specific unidirectional amplification of the sequence adjacent to the dsODN, without the bias inherent to other methods such as linear amplification-mediated (LAM)-PCR^(21, 22). We refer to our strategy as the single-tail adapter/tag (STAT)-PCR method. By performing STAT-PCR reactions using primers that anneal to each of the dsODN strands, we could obtain reads of adjacent genomic sequence on both sides of each integrated tag (FIG. 5C). Incorporation of a random 8 bp molecular barcode during the amplification process (FIG. 12) allows for correction of PCR bias, thereby enabling accurate quantitation of unique sequencing reads obtained from high-throughput sequencing.

Genome-Wide Off-Target Cleavage Profiles of CRISPR RGNs in Human Cells

We performed GUIDE-Seq with Cas9 and ten different gRNAs targeted to various endogenous human genes in either U2OS or HEK293 human cell lines (Table 5). By analyzing the dsODN integration sites (Methods), we were able to identify the precise genomic locations of DSBs induced by each of the ten RGNs, mapped to the nucleotide level (FIG. 5D). For >80% of these genomic windows, we were able to identify an overlapping target sequence that either is or is related to the on-target site (Methods). Interestingly, the total number of off-target sites we identified for each RGN varied widely, ranging from zero to >150 (FIG. 5E), demonstrating that the genome-wide extent of unwanted cleavage for any particular RGN can be considerable or minimal on the extremes. We did not observe any obvious correlation between the orthogonality of the gRNA protospacer sequence relative to the human genome (as measured by the total number of genomic sites harboring one to six mismatches) and the total number of off-target sites we observed by GUIDE-Seq (FIG. 5F). Off-target sequences are found dispersed throughout the genome (FIG. 5Gg and FIGS. 13A-J) and fall in exons, introns, and non-coding intergenic regions (FIG. 5H). Included among the off-target sequences we identified were all of the bona fide off-target sites previously known for four of the RGNs^(4, 5) (FIGS. 6A-J). More importantly, GUIDE-Seq identified a large number of new, previously unknown off-target sites that map throughout the human genome (FIGS. 5E, 5G, 6A-J and 13A-J).

TABLE 5 SEQ ID Target site name Cells Sequence NO: EMX1 U2OS GAGTCCGAGCAGAAGAAGAANGG 36 VEGFA site 1 U2OS GGGTGGGGGGAGTTTGCTCCNGG 37 VEGFA site 2 U2OS GACCCCCTCCACCCCGCCTCNGG 38 VEGFA site 3 U2OS GGTGAGTGAGTGTGTGCGTGNGG 39 RNF2 U2OS GTCATCTTAGTCATTACCTGNGG 40 FANCF U2OS GGAATCCCTTCTGCAGCACCNGG 41 HEK293 site 1 293 GGGAAAGACCCAGCATCCGTNGG 42 HEK293 site 2 293 GAACACAAAGCATAGACTGCNGG 43 HEK293 site 3 293 GGCCCAGACTGAGCACGTGANGG 44 HEK293 site 4 293 GGCACTGCGGCTGGAGGTGGNGG 45 truncated VEGFA  U2OS GTGGGGGGAGTTTGCTCCNGG 87 site 1 truncated VEGFA  U2OS GAGTGAGTGTGTGCGTGNGG 88 site 3 Truncated EMX1 U2OS GTCCGAGCAGAAGAAGAANGG 89

We next tested whether the number of sequencing reads for each off-target site identified by GUIDE-Seq (shown in FIGS. 6A-J) represents a proxy for the relative frequency of indels that would be induced by an RGN alone (i.e., in the absence of a dsODN). Examination of these sites by anchored multiplex PCR (AMP)-based next-generation sequencing for five RGNs in human U2OS cells in which nuclease components had been expressed (Methods) showed that >80% (106 out 132) harbored variable-length indels characteristic of RGN cleavage, further supporting our conclusion that GUIDE-Seq identifies bona fide RGN off-target sites (FIG. 7A). The range of indel frequencies detected ranged from 0.03% to 60.1%. Importantly, we observed positive linear correlations between GUIDE-Seq read counts and indel mutation frequencies for all five RGN off-target sites (FIGS. 7A-F). Thus, we conclude that GUIDE-Seq read counts for a given site represent a quantitative measure of the cleavage efficiency of that sequence by an RGN.

Analysis of RGN-Induced Off-Target Sequence Characteristics

Visual inspection of the off-target sites we identified by GUIDE-Seq for all ten RGNs underscores the diversity of variant sequences at which RGNs can cleave. These sites can harbor as many as six mismatches within the protospacer sequence (consistent with a previous report showing in vitro cleavage of sites bearing up to seven mismatche⁶), non-canonical PAMs (previously described NAG and NGA sequences^(5, 23) but also novel NAA, NGT, NGC, and NCG sequences), and 1 bp “bulge”-type mismatches²⁴ at the gRNA/protospacer interface (FIG. 6A-J). Protospacer mismatches tend to occur in the 5′ end of the target site but can also be found at certain 3′ end positions, supporting the notion that there are no simple rules for predicting mismatch effects based on position⁴. Interestingly, some off-target sites actually have higher sequencing read counts than their matched on-target sites (FIGS. 6A-D, 6J), consistent with our previous observations that off-target mutation frequencies can in certain cases be higher than those at the intended on-target site⁴. Notably, many of the previously known off-target sites for four of the RGNs have high read counts (FIGS. 6A-D), suggesting that previous analyses primarily identified sites that are most efficiently cleaved.

Quantitative analysis of our GUIDE-Seq data on all ten RGNs enabled us to quantify the contributions and impacts of different variables such as mismatch number, location, and type on off-target site cleavage. We found that the fraction of total genomic sites bearing a certain number of protospacer mismatches that are cleaved by an RGN decreases with increasing numbers of mismatches (FIG. 8A). In addition, sequence read counts show a general downward trend with increasing numbers of mismatches (FIG. 8B). In general, protospacer mismatches positioned closer to the 5′ end of the target site tend to be associated with smaller decreases in GUIDE-Seq read counts than those closer to the 3′ end although mismatches positioned 1 to 4 bp away from the PAM are surprisingly somewhat better tolerated than those 5 to 8 bps away (FIG. 8C). Interestingly, the nature of the mismatch is also associated with an effect on GUIDE-Seq read counts. Wobble mismatches occur frequently in the off-target sites and our analysis suggests they are associated with smaller impacts on GUIDE-Seq read counts than other non-Wobble mismatches (FIG. 8D). Consistent with these results, we find that the single factors that explain the greatest degree of variation in off-target cleavage in univariate regression analyses are mismatch number, position, and type. In contrast, other factors such as the density of proximal PAM sequences, gene expression level, or genomic position (intergenic/intronic/exonic) explain a much smaller proportion of the variance in GUIDE-Seq cleavage read counts (FIG. 8E). A combined linear regression model that considered multiple factors including mismatch position, mismatch type, gene expression level, and density of proximal PAM sequences yielded results consistent with the univariate analyses (FIG. 14). This analysis also allowed us to independently estimate that, on average and depending on their position, each additional wobble mismatch decreases off-target cleavage rates by ˜2- to 3-fold, while additional non-wobble mismatches decrease cleavage rates by ˜3-fold (FIG. 14).

Comparisons of GUIDE-Seq with Existing Off-Target Prediction Methods

Having established the efficacy of GUIDE-Seq, we next performed direct comparisons of our new method with two popular existing computational methods for predicting off-target mutation sites: the MIT CRISPR Design Tool²⁵ (crispr.mit.edu) and the E-CRISP program²⁶ (www.e-crisp.org/E-CRISP/). Both of these programs attempt to identify potential off-target sites based on certain “rules” about mismatch number and position and have been used in previous publications to identify off-target sites. In our comparisons using the ten RGNs we characterized by GUIDE-Seq, we found that both programs failed to identify the vast majority of experimentally verified off-target sites (FIGS. 9A-B). Many of these sites were missed because the E-CRISP and MIT programs simply do not consider off-targets bearing more than 3 and 4 mismatches, respectively (FIGS. 9C-D). Even among the sequences that are considered, these programs still fail to identify the majority of the bona fide off-target sites (FIG. 9C-D), highlighting their currently limited capability to account for the factors that determine whether or not cleavage will or will not occur. In particular, it is worth noting that sites missed include those with as few as one mismatch (FIGS. 9C-D), though the ranking scores assigned by the MIT program do have some predictive power among the sites it does correctly identify. Finally, it is important to note that both programs return many “false positive” sites that are not identified by GUIDE-Seq (FIGS. 9A-B). We conclude that both the MIT and the E-CRISP programs perform substantially less effectively than our GUIDE-Seq method at identifying bona fide RGN off-target sites.

Comparison of GUIDE-Seq with the ChIP-Seq Method for Determining dCas9 Binding Sites

We also sought to directly compare GUIDE-Seq with previously described ChIP-Seq methods for identifying RGN off-target sites. Four of the RGNs we evaluated by GUIDE-Seq used gRNAs that had been previously characterized in ChIP-Seq experiments with catalytically inactive Cas9 (dCas9), resulting in the identification of a large set of off-target binding site¹⁸. Direct comparisons show very little overlap between Cas9 off-target cleavage sites identified by GUIDE-Seq and dCas9 off-target binding sites identified by ChIP-Seq; among the 149 RGN-induced off-target cleavage sites we identified for the four gRNAs, only three were previously identified by the previously published dCas9 ChIP-Seq experiments using the same gRNAs (FIG. 9E). This lack of overlap is likely because dCas9 off-target binding sites are fundamentally different from Cas9 off-target cleavage sites, a hypothesis supported by our data showing that Cas9 off-target cleavage sites for these four gRNAs identified by GUIDE-Seq harbor on average far fewer mismatches than their binding sites identified by ChIP-Seq (FIG. 9F) and by the results of previous studies showing that very few dCas9 binding sites show evidence of indels in the presence of active Cas9¹⁶⁻¹⁹. Although GUIDE-Seq failed to identify the four off-target sites previously identified by ChIP-Seq and subsequently shown to be targets of mutagenesis by Cas9, we believe this is because those sites were incorrectly identified as bona fide off-target cleavage sites in that earlier study. Careful analysis of the sequencing data from that study suggests that the vast majority of indel mutations found at those sites are likely caused instead by PCR or sequencing errors and not by RGN cleavage activity (FIGS. 15A-D). Taken together, these findings demonstrate that GUIDE-Seq substantially outperforms ChIP-Seq for identification of bona fide off-target cleavage sites and provide experimental support for the idea that very few (if any) dCas9 off-target binding sites discovered by ChIP-Seq represent actual Cas9 off-target cleavage sites.

Identification of RGN-Independent DSB Hotspots in Human Cells by GUIDE-Seq

Our GUIDE-Seq experiments also unexpectedly revealed the existence of a total of 30 unique RGN-independent DSB hotspots in the U2OS and HEK293 cells used for our studies (Table 2). We uncovered these sites when analyzing genomic DNA from control experiments with U2OS and HEK293 cells in which we transfected only the dsODN without RGN-encoding plasmids (Methods). In contrast to RGN-induced DSBs that map precisely to specific base pair positions, RGN-independent DSBs have dsODN integration patterns that are more broadly dispersed at each locus in which they occur (Methods). These 30 breakpoint hotspots were distributed over many chromosomes and appeared to be present at or near centromeric or telomeric regions (FIG. 10F). Interestingly, only a small number of these DSBs (two) were common to both cell lines with the majority appearing to be cell line-specific (25 in U2OS and 7 in HEK293 cells; FIG. 10F and Table 2). To our knowledge, GUIDE-Seq is the first method to enable direct and unbiased identification of breakpoint hotspots in living human cells without the need for potentially toxic drugs (e.g., DNA replication inhibitors such as aphidicolin) to unveil their presence.

TABLE 2 Summary of RGN-independent breakpoint hotspots in human U2OS and HEK293 cells Chromo- Interval Cells some Start End (bp) U2OS chr1 121484547 121485429  882 U2OS chr1 236260170 236260754  584 U2OS chr3 197900267 197900348   81 U2OS chr4 191044096 191044100    4 U2OS chr5     10020     10477  457 U2OS chr7  16437577  16439376 1799 U2OS chr7 158129486 158129491    5 U2OS chr9 140249964 140249977   13 U2OS chr9 140610510 140610516    6 U2OS chr10  42599569  42599575    6 U2OS chr11 129573467 129573469    2 U2OS chr11 134946499 134946506    7 U2OS chr12     95427     95683  256 U2OS chr12  29944278  29946544 2266 U2OS chr16  83984266  83984271    5 U2OS chr17  63965908  63967122 1214 U2OS chr18     63765     63769    4 U2OS chr18  37381409  37381971  562 U2OS chr2   9877829   9877857   28 U2OS chr2 182140586 182140587    1 U2OS chr2 209041635 209041637    2 U2OS chr2 242838677 242838859  182 U2OS chr22  49779897  49782342 2445 U2OS chr22  49780337  49780338    1 U2OS chrX 155260204 155260352  148 HEK293 chr1 121484526 121485404  878 HEK293 chr6  58778207  58779300 1093 HEK293 chr7  61968971  61969378  407 HEK293 chr10  42385171  42385189   18 HEK293 chr10  42400389  42400394    5 HEK293 chr10  42597212  42599582 2370 HEK293 chr19  27731978  27731991   13

Participation of Both RGN-Induced and RGN-Independent DSBs in Large-Scale Genomic Rearrangements

In the course of analyzing the results of our next-generation sequencing experiments designed to identify indels at RGN-induced and RGN-independent DSBs, we also discovered that some of these breaks can participate in translocations, inversions and large deletions. The AMP method used enabled us to observe these large-scale genomic alterations because, for each DSB site examined, this method uses only nested locus-specific primers anchored at only one fixed end rather than a pair of flanking locus-specific primers (FIG. 10A). Thus, AMP-based sequencing not only identifies whether indel mutations have occurred at a DSB but it can also detect whether the DSB has been joined to another sequence.

For the five RGNs we examined, AMP sequencing revealed that RGN-induced on-target and off-target DSBs could participate in a variety of translocations (FIG. 10B). In at least one case, we could observe all four possible translocation events resulting from a pair of DSBs (FIG. 10C). When two DSBs were present on the same chromosome, we also observed large deletions and inversions (FIG. 10B). For at least one case, we observed both a large deletion between two RGN-induced breaks as well as an inversion of that same intervening sequence (FIG. 10D). Importantly, our results also revealed translocations (and deletions or inversions) between RGN-induced and RGN-independent DSBs (FIG. 10B), suggesting that the interplay between these two types of breaks needs to be considered when evaluating the off-target effects of RGNs on cellular genomes. Although our data suggest that the frequencies of these large-scale genomic rearrangements are likely to be very low, precise quantification was not possible with the sequencing depth of our existing dataset. Increasing the number of sequencing reads should increase the sensitivity of detection and enable better quantitation of these important genomic alterations.

GUIDE-Seq Profiles of RGNs Directed by Truncated gRNAs

Previous studies from our group have shown that use of gRNAs bearing truncated complementarity regions of 17 or 18 nts can reduce mutation frequencies at known off-target sites of RGNs directed by full-length gRNAs27. However, because this analysis was limited to a small number of known off-target sites, the genome-wide specificities of these truncated gRNAs (tru-gRNAs) remained undefined in our earlier experiments. We used GUIDE-Seq to obtain genome-wide DSB profiles of RGNs directed by three tru-gRNAs, each of which are shorter versions of one of the ten full-length gRNAs we had assayed above.

Our results show that in all three cases, the total number of off-target sites identified by GUIDESeq decreased substantially with use of a tru-gRNA (FIG. 11A-D). Mapping of GUIDE-Seq reads enabled us to precisely identify the cleavage locations of on-target (FIG. 11E) and off-target sites (not shown). As expected and as we observed with full-length gRNAs, included in the list of off-target sites were 10 of the 12 previously known off-target sites for RGNs directed by the three tru-gRNAs (FIGS. 11F-H). The sequences of the off-target sites we identified primarily had one or two mismatches in the protospacer but some sites had as many as four (FIGS. 11F-H). In addition, some sites had alternative PAM sequences of the forms NAG, NGA, and NTG (FIGS. 11F-H). These data provide confirmation on a genome-wide scale that truncation of gRNAs can substantially reduce off-target effects of RGNs and show how GUIDESeq can be used to assess specificity improvements for the RGN platform.

Discussion

GUIDE-Seq provides an unbiased, sensitive, and genome-wide method for detecting RGN-induced DSBs. The method is unbiased because it detects DSBs without making assumptions about the nature of the off-target site (e.g., presuming that the off-target site is closely related in sequence to the on-target site). GUIDE-Seq identifies off-target sites genome-wide, including within exons, introns, and intergenic regions, and harbored up to six protospacer mismatches and/or new mismatched PAM sites beyond the alternate NAG and NGA sequences described in earlier studies^(5, 23). For the RGNs we examined in this example, GUIDE-Seq not only successfully identified all previously known off-target sites but also unveiled hundreds of new sites as well.

Although the current lack of a practical gold standard method for comprehensively identifying all RGN off-target sites in a human cell prevents us from knowing the sensitivity of GUIDE-Seq with certainty, we believe that it very likely has a low false-negative rate for the following reasons: First, all RGN-induced blunt-ended DSBs should take up the blunt-ended dsODN by NHEJ, a hypothesis supported by the strong correlations we observe between GUIDE-Seq read counts (which measure dsODN uptake) and indel frequencies in the presence of the RGN (which measure rates DSB formation and of their mutagenic repair) (FIGS. 7B-F). We note that these correlations include over 130 sites which show a wide range of indel mutagenesis frequencies. Second, using previously identified off-target sites as a benchmark (which is the only way to gauge success at present), GUIDE-Seq was able to detect 38 out of 40 of these sites that show a range of mutagenesis frequencies extending to as low as 0.12%. The method detected all 28 previously known off-target sites for four full-length gRNAs and 10 out of 12 previously known off-target sites for three tru-gRNAs. One of the two off-target sites that was not detected showed evidence of capture in our raw data but was filtered out by our read calling algorithm because the sequencing reads were only unidirectional and originated from just one primer (Methods). (The lack of bidirectional mapping reads for this site might be due to a repetitive region on one side of the off-target site that makes it challenging to map the reads accurately.) The other undetected offtarget site has been previously.

Of note, one of the RGNs we assessed did not yield any detectable off-target effects (at the current detection limit of the GUIDE-Seq method), raising the intriguing possibility that some gRNAs may induce very few, or perhaps no, undesired mutations.

Although our validation experiments show that GUIDE-Seq can sensitively detect off-target sites that are mutagenized by RGNs with frequencies as low as 0.1%, its detection capabilities might be further improved with some simple changes. Strategies that use next-generation sequencing to detect indels are limited by the error rate of the platform (typically ˜0.1%). By contrast, GUIDE-Seq uses sequencing to identify dsODN insertion sites rather than indels and is therefore not limited by error rate but by sequencing depth. For example, we believe that the small number of sites detected in our GUIDE-Seq experiments for which we did not find indels in our sequencing validation experiments actually represent sites that likely have indel mutation frequencies below 0.1%. Consistent with this, we note that all but three of these 26 sites had GUIDE-Seq read counts below 100. Taken together, these observations suggest that we may be able to increase the sensitivity of GUIDE-Seq simply by increasing the number of sequencing reads (and by increasing the number of genomes used as template for amplification). For example, use of a sequencing platform that yields 1000-fold more reads would enable detection

Direct comparisons enabled by our GUIDE-Seq experiments show the limitations of two existing computational programs for predicting RGN off-target sites. These programs not only failed to identify bona fide off-target sites found by GUIDE-Seq but also overcalled many sites that do not show cleavage. This is not entirely surprising given that parameters used by these programs were based on more restrictive assumptions about the nature of off-target sites that do not account for greater numbers of protospacer mismatches and alternative PAM sequences identified by our GUIDE-Seq experiments. It is possible that better predictive programs might be developed in the future but doing so will require experimentally determined genome-wide off-target sites for a larger number of RGNs. Until such programs can be developed, identification of off-target sites will be most effectively addressed by experimental methods such as GUIDE-Seq.

Our experimental results elaborate a clear distinction between off-target binding site of dCas9 and off-target cleavage sites of Cas9. Comparisons of dCas9 ChIP-Seq and Cas9 GUIDE-Seq data for four different gRNAs show that there is negligible direct overlap between the two sets of sites and that the mean number of mismatches in the two classes of sites are actually substantially different. Furthermore, we show that even the small number of dCas9 binding sites previously reported to be mutagenized by Cas9 are very likely not bona fide RGN-induced cleavage sites. Taken together, our results show that the binding of dCas9 to DNA sites being captured with ChIP-Seq represents a different biological process than cleavage of DNA sites by Cas9 nuclease, consistent with the results of a recent study showing that engagement of the 5′-end of the gRNA with the protospacer is needed for efficient cleavage. Although ChIP-Seq assays will undoubtedly have a role in characterizing the genome-wide binding of dCas9 fusion proteins, the method is clearly not effective for determining genome-wide off-target cleavage sites of catalytically active RGNs.

GUIDE-Seq has several important advantages over other previously described genome-wide methods for identifying DSB sites in cells. The recently described BLESS (breaks labeling, enrichment on streptavidin and next-generation sequencing) oligonucleotide tagging method is performed in situ on fixed, permeabilized cellsL⁷. In addition to being prone to artifacts associated with cell fixation, BLESS will only capture breaks that exist at a single moment in time. By contrast, GUIDE-Seq is performed on living cells and captures DSBs that occur over a more extended period of time (days), thereby making it a more sensitive and comprehensive assay. Capture of integration-deficient lentivirus (IDLV) DNA into regions near DSBs and identification of these loci by LAM-PCR has been used to identify a small number of off-target sites for engineered zinc finger nucleases (ZFNs)²² and transcription activator-like effector nucleases (TALENs)²⁸ in human cells. However, IDLV integration events are generally low in number and widely dispersed over distances as far as 500 bps away from the actual off-target DSB^(22, 28), making it challenging both to precisely map the location of the cleavage event and to infer the sequence of the actual off-target site. In addition, LAM-PCR suffers from sequence bias and/or low efficiency of sequencing reads. Collectively, these limitations may also explain the apparent inability to detect lower frequency ZFN off-target cleavage sites by IDLV capture²⁹. By contrast, dsODNs are integrated very efficiently and precisely into DSBs with GUIDE-Seq, enabling mapping of breaks with single nucleotide resolution and simple, straightforward identification of the nuclease off-target cleavage sites. Furthermore, in contrast to LAM-PCR, our STAT-PCR method allows for efficient, unbiased amplification and sequencing of genomic DNA fragments in which the dsODN has integrated. We note that the STAT-PCR may have more general utility beyond its use in GUIDE-Seq; for example, it may be useful for studies that seek to map the integration sites of viruses on a genome-wide scale.

Although GUIDE-Seq is highly sensitive, its detection capabilities might be further improved with some simple changes. Strategies that use next-generation sequencing to detect indels are limited by the error rate of the platform (typically ˜0.1%). By contrast, GUIDE-Seq uses sequencing to identify dsODN insertion sites rather than indels and is therefore not limited by error rate but by sequencing depth. For example, we believe that the small number of sites detected in our GUIDE-Seq experiments for which we did not find indels in our sequencing validation experiments actually represent sites that likely have mutation frequencies below 0.1%. Consistent with this, we note that all but 3 of these 26 sites had GUIDE-Seq read counts below 100. Taken together, these observations suggest that we may be able to increase the sensitivity of GUIDE-Seq simply by increasing the number of sequencing reads (and by increasing the number of genomes used as template for amplification). For example, use of a sequencing platform that yields 1000-fold more reads would enable detection of sites with mutagenesis frequencies three orders of magnitude lower (i.e., 0.0001%), and we expect further increases to occur with continued improvements in technology.

An unexpected result of our experiments was the realization that GUIDE-Seq could also identify breakpoint hotspots that occur in cells even in the absence of RGNs. We believe that these DSBs are not just an artifact of GUIDE-Seq because our AMP-based sequencing experiments verified not only capture of dsODNs but also the formation of indels at these sites. Of note, many hotspots are unique to each of the two cell lines examined in our study, but some also appear to be common to both. It will be interesting in future studies to define the parameters that govern why some sites are breakpoint hotspots in one cell type but not another. Also, because our results show that these breakpoint hotspots can participate in translocations, the existence of cell-type-specific breakpoint hotspots might help to explain why certain genomic rearrangements only occur in specific cell types but not others. To our knowledge, GUIDE-Seq is the first method to be described that can identify breakpoint hotspots in living human cells without the need to add drugs that inhibit DNA replication²⁷. Therefore, we expect that it will provide a useful tool for identifying and studying these breaks.

Our work establishes the most comprehensive qualitative approach described to date for identifying translocations induced by RGNs. AMP-based targeted sequencing of RGN-induced and RGN-independent DSB sites discovered by GUIDE-Seq can find large-scale genomic rearrangement that includes translocations, deletions, and inversions involving both classes of sites, highlighting the importance of considering both classes of breaks when identifying large-scale genomic rearrangements. In addition, presumably not all RGN-induced or RGN-independent DSBs will participate in large-scale alterations and understanding why some sites do and other sites do not contribute to these rearrangements will be an important area for further research.

GUIDE-Seq will also provide an important means to evaluate specificity improvements to the RGN platform on a genome-wide scale. In this report, we used GUIDE-Seq to show how the implementation of truncated gRNAs can reduce off-target effects on a genome-scale, extending earlier results from our group that this approach can reduce mutations at known off-target sites of a matched full-length gRNA³⁰. It might also be adapted to assess the genome-wide specificities of alternative Cas9 nucleases from other bacteria or archaea, or of nucleases such as dimeric ZFNs, TALENs, and CRISPR RNA-guided FokI nucleases^(31, 32) that generate 5′ overhangs or paired Cas9 nickases^(33, 34) that generate 5′ or 3′ overhangs; however, extending GUIDE-Seq to detect these other types of DSBs will undoubtedly require additional modification and optimization of the dsODN to ensure its efficient capture into such breaks. The method might also be used to assess the specificities of alternative Cas9 nucleases from other bacteria or archaea₃₅. One important caveat is the need to examine a large number of gRNAs before broadly drawing conclusions about the specificity of any new Cas9 platform because we found very wide variability in the number of off-target sites for the ten gRNAs we assessed.

Our exemplary approach using GUIDE-Seq and AMP-based sequencing establishes a new gold standard for the evaluation of off-target mutations and genomic rearrangements induced by RGNs. We expect that GUIDE-Seq can be extended for use in any cell in which NHEJ is active and into which the required components can be efficiently introduced; for example, we have already achieved efficient dsODN integration in human K562 and mouse embryonic stem cells (data not shown). Most importantly, the strategies outlined here can be used as part of a rigorous pre-clinical pathway for objectively assessing the potential off-target effects of any RGNs proposed for therapeutic use, thereby substantially improving the prospects for use of these reagents in the clinic.

Example 3

Additional experiments were performed to explore the requirements for the dsODNs that can be used in some embodiments of the present methods.

The following dsODNs were used in the experiments in Example 3:

SEQ ID dsODN type Sequence NO: phosphorylated,  /5Phos/N*N*NNGTTTAATTGAGTT 47 5′ overhang, GTCATATGTTAATAACGGT*A*T 5′ end-protected F phosphorylated,  /5Phos/N*N*NNATACCGTTATTAA 48 5′ overhang, CATATGACAACTCAATTAA*A*C 5′ end-protected R phosphorylated,  /5Phos/G*T*TTAATTGAGTTGTCAT 49 3′ overhang, ATGTTAATAACGGTATNN*N*N 3′ end-protected F phosphorylated,  /5Phos/A*T*ACCGTTATTAACATA 50 3′ overhang, TGACAACTCAATTAAACNN*N*N 3′ end-protected R phosphorylated,  /5Phos/G*T*TTAATTGAGTTGTCAT  1 blunt, 5′ and ATGTTAATAACGGT*A*T 3′ end-protected F phosphorylated,  /5Phos/A*T*ACCGTTATTAACATA  2 blunt, 5′ and TGACAACTCAATTAA*A*C 3′ end-protected R phosphorylated,  /5Phos/GTTTAATTGAGTTGTCATA 51 blunt, 3′ TGTTAATAACGGT*A*T end-protected F phosphorylated,  /5Phos/ATACCGTTATTAACATATG 52 blunt, 3′ ACAACTCAATTAA*A*C end-protected R /5Phos/ indicates 5′ phosphorylation *indicates phosphorothioate linkage All oligos were annealed in STE.

First, the integration frequencies of 3 types of dsODNs using TALENs, ZFNs, and RFNs targeted against EGFP were evaluated. 2E5 U2OS-EGFP cells were nucleofected with 500 ng each TALEN monomer (1 ug total), 500 ng each ZFN monomer (1 ug total), or 325 ng multiplex gRNA plasmid and 975 ng FokI-dCas9 expression plasmid and 100 pmol of dsODN. The three dsODNs used had either a 4-bp 5′ overhang with 5′ phosphorothioate linkages, a 4-bp 3′ overhang with 3′ phosphorothioate linkages, or were blunt with 5 ‘and 3’ phosphorothioate linkages. All dsODNs were 5′ phosphorylated. Integration frequency was estimated with NdeI restriction fragment length polymorphism (RFLP) assay and quantified using capillary electrophesis; briefly, target sites were amplified by PCRs from isolated genomic DNA. PCRs were digested with NdeI restriction enzyme (20 U) at 37° C. for 3 hours and purified with 1.8× AMPURE XP automated PCR purification. Purified cleavage products run and quantified by a QIAXCEL capillary electrophoresis instrument (Qiagen). FIG. 16A shows that blunt-ended dsODNs that were 5′ phosphorylated and 3′ phosphorothioated had the highest integration rates.

The same oligos (SEQ ID NOs:1 and 2) used above were transfected into U2OS cells (program DN-100) in 20 μl Solution SE (Lonza) on a Lonza Nucleofector 4-D according to the manufacturer's instructions. 500 ng of each TALEN monomer (TAL1252/TAL1301 for CCR5 and TAL2294/2295 for APC) and 100 pmol of dsODN were transfected. FIGS. 16B-C show evidence of efficient integration of a blunt, 5′-phosphorylated, 34-bp double-stranded oligodeoxynucleotide (dsODN) (oSQT685/686) into double-stranded breaks (DSBs) induced by TALENs at 2 endogenous target sites, CCR5 and APC in U2OS cells, as determined by NdeI restriction fragment length polymorphism (RFLP) analysis (described above) or T7E1 assay (briefly, target sites were amplified by PCRs from isolated genomic DNA. PCRs were purified with 1.8× AMPURE XP automated PCR purification. Purified PCR product (200 ng) was hybridized according to the following protocol: 95° C. for 5 minutes, 95-85° C. at −2° C./s, 85-25° C. at −1° C./10 s; hold at 10° C. T7 Endonuclease I (10 U) was added to the reactions, which were incubated at 37° C. for 15 minutes. The reactions were stopped by adding EDTA (25 mM) and purified with 1.8× AMPURE XP automated PCR purification. Purified cleavage products run and quantified by a QIAXCEL capillary electrophoresis instrument (Qiagen)).

Additional experiments were conducted with 2E5 U2OS-EGFP cells were nucleofected with 325 ng multiplex gRNA plasmid and 975 ng FokI-dCas9 expression plasmid and 100 pmol of dsODN. Additionally, 3E5 Mouse ES cells were nucleofected with 200 ng single gRNA plasmid and 600 ng Cas9 expression plasmid, and 100 pmol dsODN. Two dsODNs were compared: 1) blunt, phosphorylated, 5′ and 3′ phosphorothioate-modified and 2) blunt, phosphorylated, only 3′ phosphorothioate-modified. Integration frequency was estimated with NdeI restriction fragment length polymorphism (RFLP) assay and quantified using capillary electrophesis.

The experiments, conducted with dimeric RNA-guided FokI nucleases in human U2OS cells (FIG. 17A), or with standard Cas9 in mouse ES cells (FIG. 17B), showed that the dsODNs with only 3′ phosphorothioate modifications had the highest rates of integration.

Additional experiments were performed to test different concentrations of 3′ phosphorothioate modified oligo in mouse ES cells. 3E5 Mouse ES cells were nucleofected with 200 ng single gRNA plasmid and 600 ng Cas9 expression plasmid, and varying amounts of dsODN as described below. Blunt, phosphorylated, only 3′ phosphorothioate-modified dsODNs were used in this experiment. Annealed oligos were purified using a SEPHADEX G-25 gel filtration resin column in a comparison between purified and unpurified dsODN. dsODNs were tested at concentrations of 1, 2, 5, 10, 25, 50, and 100 pmol. Integration frequency was estimated with NdeI restriction fragment length polymorphism (RFLP) assay and quantified using capillary electrophesis. The results, shown in FIGS. 18A and 18B, indicated that 50 pmol or 100 pmol provided the best activity. Purification of the oligo through a SEPHADEX G-25 gel filtration resin column did not improve rates significantly (see FIGS. 18A and 18B). Mutagenesis frequency was estimated by T7E1 assay, which showed that the general rate of disruption was high, even in the presence of 3′-modified dsODN.

The length of the dsODNs was also evaluated. FIGS. 20A-B show that longer (e.g., 60 bp) dsODN tags integrated efficiently at sites of CRISPR-Cas9 induced DSBs. These longer dsODNs can be used to improve the accuracy of GUIDE-seq by enabling bioinformatic filtering of PCR amplification artifacts. These sequences could be recognized as any that did not contain sequences present in the longer tag.

SEQ ID ssODN Sequence NO: oSQT1255 /5Phos/ 53 C*C*GCTTGCAGAGGGTATATTTGGTTAT CATATG GGACGAGTAGACTGAGATGAAGGTT*T*A oSQT1256 /5Phos/ 54 T*A*AACCTTCATCTCAGTCTACTCGTCC CATATG ATAACCAAATATACCCTCTGCAAGC*G*G oSQT1257 /5Phos/ 55 A*G*GACTGCATTCTTGTATACTTAGACT CATATG TTCCTCTGGTACCGCGTAGATGTTT*A*C oSQT1258 /5Phos/ 56 G*T*AAACATCTACGCGGTACCAGAGGAA CATATG AGTCTAAGTATACAAGAATGCAGTC*C*T oSQT1259 /5Phos/ 57 A*C*CAATCAGTCACGAGCCTAGGAGATT CATATG GGTAAGAGAGTCACATAATGCTTCC*G*G oSQT1260 /5Phos/ 58 C*C*GGAAGCATTATGTGACTCTCTTACC CATATG AATCTCCTAGGCTCGTGACTGATTG*G*T *indicates phosphorothioate linkage

These experiments show that the efficiency of dsODN tag uptake can be increased by using oligos that are modified only on the 3′ ends rather than on both the 5′ and 3′ ends, that are longer, and that efficient capture of the dsODN tag occurs in a variety of cell lines, including cells that are not from a transformed cancer cell line (e.g., mouse ES cells).

Example 4

In this Example, a biotinylated version of the GUIDE-seq dsODN tag was used as a substrate for integration into the sites of genomic DSBs. As shown in Example 4, it was possible to integrate such an oligo efficiently. The experiments were performed as described above, using a biotinylated dsODN, obtained from IDT DNA.

SEQ ID dsODN Sequence NO: oSQT1261 /5Phos/G*T*TTAATTGAG/iBiodT/TGTCATATG 59 TTAATAACGGT*A*T oSQT1262 /5Phos/A*T*ACCGTTA/iBiodT/TAA CATATG 60 ACAACTCAATTAA*A*C iBiodT - biotin dT tag *indicates phosphorothioate linkage

FIGS. 19A-B provide evidence for efficient integration of biotinylated dsODN tag into double-stranded breaks (DSBs) induced by Cas9 at 3 endogenous target sites, VEGFA3, EMX1, and FANCF1 in U2OS cells. This advancement could enable direct physical capture of tagged fragments by exploiting the tight binding affinity of biotin and streptavidin. (A) RFLP analysis shows % integration rates of biotinylated dsODN (oSQT1261/1262), compared to the standard dsODN (oSQT685/686) into DSBs induced by Cas9 at 3 endogenous sites, VEGFA3, EMX1, and FANCF1 in U2OS cells. (B) T7EI shows % estimated mutagenesis frequencies with biotinylated dsODN (oSQT1261/1262), compared to the standard dsODN (oSQT685/686) at 3 endogenous sites, VEGFA3, EMX1, and FANCF1 in U2OS cells.

Assuming that the biotinylation is preserved in cells, it can be used to physically pulldown DNA fragments including the biotinyulated ssODNs, and to sequence and map the captured fragments.

Example 5

In this Example, an exemplary GUIDE-Seq method is used with variant Cas9 proteins.

Variant Streptococcus pyogenes Cas9 (SpCas9) and Staphylococcus aureus Cas9 (SaCas9) proteins were generated as described in U.S. Ser. No. 61/127,634 and 62/165,517, incorporated herein by reference, and in Kleinstiver et al., “Engineered CRISPR-Cas9 nucleases with altered PAM specificities.” Nature (2015) doi:10.1038/nature14592. Off-target effects were evaluated as described above.

FIG. 21 shows the number of off-target cleavage sites identified by GUIDE-seq for engineered SpCas9 variants comprising mutations at D1135V/R1335Q/T1337R (VQR variant) or D1135V/G1218R/R1335E/T1337R (VRER variant) using sgRNAs targeting EMX1, FANCF, RUNX1, VEGFA, or ZNF629 (see table 4 for sequences). This demonstrates that GUIDE-seq can also be used to profile the genome-wide specificity of engineered versions of Cas9. GUIDE-seq was also used to determine specificity profiles of the VQR and VRER SpCas9 variants in human cells by targeting endogenous sites containing NGA or NGCG PAMs.

TABLE 4 Spacer SEQ SEQ length ID Sequence with extended ID Name (nt) Spacer Sequence NO: PAM NO: EMX1 NGA 4-20 20 GCCACGAAGCAGGCCAATGG 61 GCCACGAAGCAGGCCAATGGGGAG 62 FANCF NGA 1- 20 GAATCCCTTCTGCAGCACCT 63 GAATCCCTTCTGCAGCACCTGGAT 64 20 FANCF NGA 3- 20 GCGGCGGCTGCACAACCAGT 65 GCGGCGGCTGCACAACCAGTGGAG 66 20 FANCF NGA 4- 20 GGTTGTGCAGCCGCCGCTCC 67 GGTTGTGCAGCCGCCGCTCCAGAG 68 20 RUNX1 NGA 1- 20 GGTGCATTTTCAGGAGGAAG 69 GGTGCATTTTCAGGAGGAAGCGAT 70 20 RUNX1 NGA 3- 20 GAGATGTAGGGCTAGAGGGG 71 GAGATGTAGGGCTAGAGGGGTGAG 72 20 VEGFA NGA 1- 20 GCGAGCAGCGTCTTCGAGAG 73 GCGAGCAGCGTCTTCGAGAGTGAG 74 20 ZNF629 NGA 1- 20 GTGCGGCAAGAGCTTCAGCC 75 GTGCGGCAAGAGCTTCAGCCAGAG 76 20 FANCF NGCG 3- 20 GCAGAAGGGATTCCATGAGG 77 GCAGAAGGGATTCCATGAGGTGCG 78 20 FANCF NGCG 4- 19 GAAGGGATTCCATGAGGTG 79 GAAGGGATTCCATGAGGTGCGCG 80 19 RUNX1 NGCG 1- 19 GGGTGCATTTTCAGGAGGA 81 GGGTGCATTTTCAGGAGGAAGCG 82 19 VEGFA NGCG 1- 20 GCAGACGGCAGTCACTAGGG 83 GCAGACGGCAGTCACTAGGGGGCG 84 20 VEGFA NGCG 2- 20 GCTGGGTGAATGGAGCGAGC 85 GCTGGGTGAATGGAGCGAGCAGCG 86 20

FIG. 22 shows changes in specificity between wild-type and D1135E SpCas9 variants at off-target sites detected using an exemplary GUIDE-seq method as described herein. GUIDE-seq was also used to determine read-count differences between wild-type SpCas9 and D1135E at 3 endogenous human cell sites.

GUIDE-seq dsODN tag integration was also performed at 3 genes with wild-type and engineered Cas9 D1135E variant. The results, shown in FIGS. 23A-B, provide additional evidence that GUIDE-seq can be used to profile engineered Cas9 variants.

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Other Embodiments

It is to be understood that while the invention has been described in conjunction with the detailed description thereof, the foregoing description is intended to illustrate and not limit the scope of the invention, which is defined by the scope of the appended claims. Other aspects, advantages, and modifications are within the scope of the following claims. 

What is claimed is:
 1. A method for detecting double stranded breaks (DSBs) in genomic DNA of a cell, the method comprising: contacting the cell with a double-stranded oligodeoxynucleotide (dsODN), wherein both strands of the dsODN are orthogonal to the genome of the cell; preferably, the 5′ ends of the dsODN are phosphorylated; and also preferably, phosphorothioate linkages are present on both 3′ ends, or two phosphorothioate linkages are present on both 3′ ends and both 5′ ends; expressing or activating the exogenous engineered nuclease in the cell, for a time sufficient for the nuclease to induce DSBs in the genomic DNA of the cell, and for the cell to repair the DSBs, integrating a dsODN at one or more DSBs; amplifying a portion of genomic DNA comprising an integrated dsODN; and sequencing the amplified portion of the genomic DNA, thereby detecting a DSB in the genomic DNA of the cell.
 2. The method of claim 1, wherein amplifying a portion of the genomic DNA comprises: fragmenting the DNA; ligating ends of the fragmented genomic DNA from the cell with a universal adapter; performing a first round of polymerase chain reaction (PCR) on the ligated DNA with a primer complementary to the integrated dsODN (primer A) and a primer complementary to the universal adapter (primer B); then performing a second round of PCR using a 3′ nested primer complementary to primer A (primer C), a 3′ nested primer complementary to primer B (primer D), and a primer complementary to primer D (primer E).
 3. The method of claim 2, wherein primer E comprises one or more of: a purification or binding sequence; and/or an identification sequence.
 4. The method of claim 1, wherein the engineered nuclease is selected from the group consisting of meganucleases, zinc-finger nucleases, transcription activator effector-like nucleases (TALEN), and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas RNA-guided nucleases (CRISPR/Cas RGNs).
 5. The method of claim 1, wherein the DSBs are off-target DSBs.
 6. The method of claim 1, wherein the DSBs were induced by an exogenous engineered nuclease.
 7. A method of determining which of a plurality of guide RNAs is most specific, the method comprising: contacting a first population of cells with a first guide RNA and a double-stranded oligodeoxynucleotide (dsODN), wherein the dsODN is preferably between 15 and 50 nts long or between 50 and 75 nts long, wherein both strands of the dsODN are orthogonal to the genome of the cell; preferably, the 5′ ends of the dsODN are phosphorylated; and also preferably, phosphorothioate linkages are present on both 3′ ends, or two phosphorothioate linkages are present on both 3′ ends and both 5′ ends; expressing or activating an exogenous Cas9 engineered nuclease in the first population of cells, for a time sufficient for the nuclease to induce DSBs in the genomic DNA of the cells, and for the cells to repair the DSBs, integrating a dsODN at one or more DSBs; amplifying a portion of genomic DNA from the first population of cells comprising an integrated dsODN; and sequencing the amplified portion of the genomic DNA from the first population of cells; determining a number of sites at which the dsODN integrated into the genomic DNA of the first population of cells; contacting a second population of cells with a second guide RNA and a double-stranded oligodeoxynucleotide (dsODN), wherein the dsODN is preferably between 15 and 50 nts long, wherein both strands of the dsODN are orthogonal to the genome of the cell; preferably, the 5′ ends of the dsODN are phosphorylated; and also preferably, phosphorothioate linkages are present on both 3′ ends, or two phosphorothioate linkages are present on both 3′ ends and both 5′ ends; expressing or activating an exogenous Cas9 engineered nuclease in the second population of cells, for a time sufficient for the nuclease to induce DSBs in the genomic DNA of the second population of cells, and for the cells to repair the DSBs, integrating a dsODN at one or more DSBs; amplifying a portion of genomic DNA comprising an integrated dsODN from the second population of cells; and sequencing the amplified portion of the genomic DNA from the second population of cells; determining a number of sites at which the dsODN integrated into the genomic DNA of the second population of cells; comparing the number of sites at which the dsODN integrated into the genomic DNA of the first population of cells to the number of sites at which the dsODN integrated into the genomic DNA of the second population of cells; wherein the dsODN that integrated at fewer (off-target) sites is more specific.
 8. The method of claim 1, wherein the cell is a mammalian cell.
 9. The method of claim 1, wherein the engineered nuclease is a Cas9 nuclease, and the method also includes expressing in the cells a guide RNA that directs the Cas9 nuclease to a target sequence in the genome.
 10. The method of claim 1, wherein the dsODN is 30-35 nts long or 60-65 nts long.
 11. The method of claim 1, wherein the dsODN is biotinylated.
 12. The method of claim 11, wherein the method comprises: shearing the genomic gDNA into fragments; and isolating fragments comprising a dsODN by binding to the biotin.
 13. The method of claim 1, wherein the dsODN is blunt-ended.
 14. The method of claim 1, wherein the dsODN has 1, 2, 3, or 4 nts overhanging on the 5′ end.
 15. The method of claim 1, wherein the dsoDN is phosphorylated on the 5′ ends, and phosphorothioated on the 3′ ends.
 16. The method of claim 1, wherein the dsODN contains a randomized DNA barcode.
 17. The method claim 1, comprising: shearing the genomic gDNA into fragments; and preparing the fragments for sequencing by end-repair/a-tailing/ligation of a single-tailed sequencing adapter. 